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Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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2
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Nie K, Zhang J, Xu H, Ren K, Yu C, Zhang Q, Li F, Yang Q. Reverse design of haptens based on antigen spatial conformation to prepare anti-capsaicinoids&gingerols antibodies for monitoring of gutter cooking oil. Food Chem X 2024; 22:101273. [PMID: 38524780 PMCID: PMC10957407 DOI: 10.1016/j.fochx.2024.101273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/24/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Rapid simultaneous detection of multi-component adulteration markers can improve the accuracy of identification of gutter cooking oil in edible oil, which is made possible by broad-spectrum antibody (bs-mAb). This study used capsaicinoids (CPCs) and gingerol derivatives (GDs) as adulteration markers, and two broad-spectrum haptens (bs-haptens) were designed and synthesized based on a reverse design strategy of molecular docking. Electrostatic potential (ESP) and monoclonal antibodies (mAbs) preparation verified the strategy's feasibility. To further investigate the recognition mechanism, five other reported antigens and mAbs were also used. Finally, the optimal combination (Hapten 5-OVA/1-F12) and key functional groups (f-groups) were determined. The half maximal inhibitory concentration (IC50) for CPCs-GDs was between 88.13 and 499.16 ng/mL. Meanwhile, a preliminary lateral flow immunoassay (LFIA) study made practical monitoring possible. The study provided a theoretical basis for the virtual screening of bs-haptens and simultaneous immunoassay of multiple exogenous markers to monitor gutter oil rapidly and accurately.
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Affiliation(s)
- Kunying Nie
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Jiali Zhang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Haitao Xu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Keyun Ren
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Chunlei Yu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Qi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
- Laboratory of Risk Assessment for Oil-seeds Products, Wuhan, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Falan Li
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Qingqing Yang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
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3
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Cao Q, Mei S, Mehmood A, Sun Y, Chen X. Inhibition of pancreatic lipase by coffee leaves-derived polyphenols: A mechanistic study. Food Chem 2024; 444:138514. [PMID: 38310782 DOI: 10.1016/j.foodchem.2024.138514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/06/2024]
Abstract
The suppression of pancreatic lipase has been employed to mitigate obesity. This study explored the mechanism of coffee leaf extracts to inhibit pancreatic lipase. The ethyl acetate fraction derived from coffee leaves (EAC) exhibited the highest inhibitory capacity with a half-maximal inhibitory concentration (IC50) of 0.469 mg/mL and an inhibitor constant (Ki) of 0.185 mg/mL. This fraction was enriched with 3,5-dicaffeoylquinic acid (3,5-diCQA, 146.50 mg/g), epicatechin (87.51 mg/g), and isoquercetin (48.29 mg/g). EAC inhibited lipase in a reversible and competitive manner, and quenched its intrinsic fluorescence through a static mechanism. Molecular docking revealed that bioactive compounds in EAC bind to key amino acid residues (HIS-263, PHE-77, and SER-152) located within the active cavity of lipase. Catechin derivatives play a key role in the lipase inhibitory activity within EAC. Overall, our findings highlight the promising potential of coffee leaf extract as a functional ingredient for alleviating obesity through inhibition of lipase.
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Affiliation(s)
- Qingwei Cao
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu 212013, PR China.
| | - Suhuan Mei
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu 212013, PR China
| | - Arshad Mehmood
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu 212013, PR China; Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu 212013, PR China
| | - Yu Sun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu 212013, PR China
| | - Xiumin Chen
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu 212013, PR China; Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu 212013, PR China; International Joint Research Laboratory of Intelligent Agriculture and Agri-products Processing, Jiangsu University, Zhenjiang 212013, PR China.
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Tao Y, Xu J, Zhang N, Jiao X, Yan B, Zhao J, Zhang H, Chen W, Fan D. Unraveling the binding mechanisms of transglutaminase and substrate subjected to microwaves: Molecular docking and molecular dynamic simulations. Food Chem 2024; 443:138568. [PMID: 38301564 DOI: 10.1016/j.foodchem.2024.138568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
Previous studies showed that transglutaminase (TGase) and microwaves acted synergistically to improve the functional properties of proteins. The mechanism behind this has yet to be elucidated. In this study, the phenomenon of microwaves enhancing TGase activity was experimentally validated. Molecular docking and molecular dynamics simulations revealed that moderate microwaves (105 and 108 V/m) increased the structural flexibility of TGase and promoted the orientation of the side chain carboxylate anion group on Asp255, driving the reaction forward. Also, TGase underwent partial transformation from α-helix to turns or coils at 105 and 108 V/m, exposing more residues in the active site and facilitating the binding of the substrate (CBZ-Gln-Gly) to TGase. However, 109 V/m microwaves completely destroyed the TGase structure, inactivating the enzyme. This study provides insights into the molecular mechanisms underlying the interactions between TGase and substrate subjected to microwaves, promoting the future applications of TGase and microwaves in food processing.
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Affiliation(s)
- Yuan Tao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jiawei Xu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Nana Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xidong Jiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Bowen Yan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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5
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Feng X, Wang R, Lu J, Du Q, Cai K, Zhang B, Xu B. Taste properties and mechanism of umami peptides from fermented goose bones based on molecular docking and molecular dynamics simulation using umami receptor T1R1/T1R3. Food Chem 2024; 443:138570. [PMID: 38301563 DOI: 10.1016/j.foodchem.2024.138570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/13/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
Umami peptides are valuable taste substances due to their exceptional taste and beneficial properties. In this study, purification of fermented goose bone broth was performed using continuous chromatography and sensory analysis, and after identification through nano-LC-MS/MS, four umami peptides were screened out by umami activity prediction and molecular docking, which are VGYDAE, GATGRDGAR, GETGEAGER, and GETGEAGERG derived from collagen. Sensory analysis indicated that they were also umami-enhancing, with thresholds ranging from 0.41 to 1.15 mmol/L, among which GER9 was the best. Combining the results of docking and molecular dynamics simulation, it was known that hydrogen bond and electrostatic interactions were vital in driving the umami formation. Moreover, Glu, Ser, and Asp of umami receptor T1R1/T1R3 were the key residues for the binding between four umami peptides and T1R1/T1R3. These findings provide novel insights into the high-value utilization of goose bones and offer profound theoretical guidance for understanding the umami mechanism.
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Affiliation(s)
- Xinrui Feng
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Ran Wang
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Jingnan Lu
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Qingfei Du
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Kezhou Cai
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, Hefei University of Technology, Hefei 230601, China.
| | - Bao Zhang
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, Hefei University of Technology, Hefei 230601, China.
| | - Baocai Xu
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, Hefei University of Technology, Hefei 230601, China
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Cytarska J, Szulc J, Kołodziej-Sobczak D, Nunes JA, da Silva-Júnior EF, Łączkowski KZ. Cyrene™ as a tyrosinase inhibitor and anti-browning agent. Food Chem 2024; 442:138430. [PMID: 38241986 DOI: 10.1016/j.foodchem.2024.138430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
The tyrosinase pathway takes part in the enzymatic process of food browning and is primarily responsible for food spoilage - manifesting itself from a decrease in its nutritional value to a deterioration of taste, which consequently leads to a gradual loss of shelf life. Finding safe and bio-based tyrosinase inhibitors and anti-browning agents may be of great importance in agriculture and food industries. Herein, we showed that Cyrene™ exhibits tyrosinase inhibitory activity (IC50: 268.2 µM), the 1.44 times higher than ascorbic acid (IC50: 386.5 μM). Binding mode studies demonstrated that the carbonyl oxygen of Cyrene™ coordinates with both copper ions. Surprisingly, both hydroxyl groups of Cyrene gem-diol perform a monodentate binding mode with both copper ions, at similar distances. This fact suggests that both compounds could have a similar binding mode and, as consequence, similar biological activities in tyrosinase inhibition assays and anti-browning activities.
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Affiliation(s)
- Joanna Cytarska
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Joanna Szulc
- Department of Food Industry Technology and Engineering, Bydgoszcz University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Dominika Kołodziej-Sobczak
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland.
| | - Jéssica Alves Nunes
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, AC Simões Campus, Lourival Melo Mota Avenue, s/n, 57072-970 Maceió, Alagoas, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, AC Simões Campus, Lourival Melo Mota Avenue, s/n, 57072-970 Maceió, Alagoas, Brazil
| | - Krzysztof Z Łączkowski
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland.
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Zhuang M, Li J, Wang A, Li G, Ke S, Wang X, Ning M, Sheng Z, Wang B, Zhou Z. Structurally manipulated antioxidant peptides derived from wheat bran: Preparation and identification. Food Chem 2024; 442:138465. [PMID: 38266414 DOI: 10.1016/j.foodchem.2024.138465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
Bioactive peptide's development is facing two challenges in terms of its lower yield and limited understanding of structurally orientated functionality. Therefore, peptides were prepared from wheat bran via a cocktail enzyme for achieving a higher level of hydrophobic amino acids than traditional method. The obtained peptides exhibited great antioxidant activities against H2O2-induced oxidative stress in HepG2 cells. Among them, 91 bioactive peptides were selected through the virtual screening, and their N-terminal and C-terminal contained many hydrophobic amino acids. Then the peptides with capacity to interact with Keap1 were identified by in silico simulation, because Keap1 acts as a sensor of redox insults. The results revealed that peptides DLDW and DLGL demonstrated the highest binding affinities, and a bridge was formed between Asp of DLGL and Arg415 of Klech domain, contributing to interfering Keap1-Nrf2 interaction. These findings implied a potential application of wheat bran peptides as nutraceuticals and health-promoting ingredients.
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Affiliation(s)
- Min Zhuang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jiaqing Li
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anqi Wang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Gaoheng Li
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Sheng Ke
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xuanyu Wang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ming Ning
- Key Laboratory for Processing and Quality Safety Control of Characteristic Agricultural Products, the Ministry of Agriculture and Rural Affairs, Shihezi University, Shihezi 832003, China
| | - Zhanwu Sheng
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 570101, China
| | - Bing Wang
- Gulbali Institute-Agriculture Water Environment, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Zhongkai Zhou
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory for Processing and Quality Safety Control of Characteristic Agricultural Products, the Ministry of Agriculture and Rural Affairs, Shihezi University, Shihezi 832003, China; Gulbali Institute-Agriculture Water Environment, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.
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Quayum ST, Esha NJI, Siraji S, Abbad SSA, Alsunaidi ZH, Almatarneh MH, Rahman S, Alodhayb AN, Alibrahim KA, Kawsar SM, Uddin KM. Exploring the effectiveness of flavone derivatives for treating liver diseases: Utilizing DFT, molecular docking, and molecular dynamics techniques. MethodsX 2024; 12:102537. [PMID: 38299040 PMCID: PMC10828815 DOI: 10.1016/j.mex.2023.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/24/2023] [Indexed: 02/02/2024] Open
Abstract
In exploring nature's potential in addressing liver-related conditions, this study investigates the therapeutic capabilities of flavonoids. Utilizing in silico methodologies, we focus on flavone and its analogs (1-14) to assess their therapeutic potential in treating liver diseases. Molecular change calculations using density functional theory (DFT) were conducted on these compounds, accompanied by an evaluation of each analog's physiochemical and biochemical properties. The study further assesses these flavonoids' binding effectiveness and locations through molecular docking studies against six target proteins associated with human cancer. Tropoflavin and taxifolin served as reference drugs. The structurally modified flavone analogs (1-14) displayed a broad range of binding affinities, ranging from -7.0 to -9.4 kcal mol⁻¹, surpassing the reference drugs. Notably, flavonoid (7) exhibited significantly higher binding affinities with proteins Nrf2 (PDB:1 × 2 J) and DCK (PDB:1 × 2 J) (-9.4 and -8.1 kcal mol⁻¹) compared to tropoflavin (-9.3 and -8.0 kcal mol⁻¹) and taxifolin (-9.4 and -7.1 kcal mol⁻¹), respectively. Molecular dynamics (MD) simulations revealed that the docked complexes had a root mean square deviation (RMSD) value ranging from 0.05 to 0.2 nm and a root mean square fluctuation (RMSF) value between 0.35 and 1.3 nm during perturbation. The study concludes that 5,7-dihydroxyflavone (7) shows substantial promise as a potential therapeutic agent for liver-related conditions. However, further validation through in vitro and in vivo studies is necessary. Key insights from this study include:•Screening of flavanols and their derivatives to determine pharmacological and bioactive properties using ADMET, molinspiration, and pass prediction analysis.•Docking of shortlisted flavone derivatives with proteins having essential functions.•Analysis of the best protein-flavonoid docked complexes using molecular dynamics simulation to determine the flavonoid's efficiency and stability within a system.
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Affiliation(s)
- Syeda Tasnim Quayum
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Nusrat Jahan Ikbal Esha
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Siam Siraji
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Sanaa S. Al Abbad
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Zainab H.A. Alsunaidi
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah N. Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khuloud A. Alibrahim
- Department of Chemistry, Princess Nora bint Abdulrahman University, College of Science, Riyadh, Al Riyadh, 11671, Saudi Arabia
| | - Sarkar M.A. Kawsar
- Lab of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh
| | - Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
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9
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Meng P, Wang Y, Huang Y, Liu T, Ma M, Han J, Su X, Li W, Wang Y, Lu C. A strategy to boost xanthine oxidase and angiotensin converting enzyme inhibitory activities of peptides via molecular docking and module substitution. Food Chem 2024; 442:138401. [PMID: 38219570 DOI: 10.1016/j.foodchem.2024.138401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/03/2024] [Accepted: 01/06/2024] [Indexed: 01/16/2024]
Abstract
Molecular docking and activity evaluation screened the dipeptide module GP with low xanthine oxidase (XOD) inhibitory activity and modules KE and KN with high activity, and identified them as low- and high-contribution modules, respectively. We hypothesized the substitution of low-contribution modules in peptides with high contributions would boost their XOD inhibitory activity. In the XOD inhibitory peptide GPAGPR, substitution of GP with both KE and KN led to enhanced affinity between the peptides and XOD. They also increased XOD inhibitory activity (26.4% and 10.3%) and decreased cellular uric acid concentrations (28.0% and 10.4%). RNA sequencing indicated that these improvements were attributable to the inhibition of uric acid biosynthesis. In addition, module substitution increased the angiotensin-converting enzyme inhibitory activity of GILRP and GAAGGAF by 84.8% and 76.5%. This study revealed that module substitution is a feasible strategy to boost peptide activity, and provided information for the optimization of hydrolysate preparation conditions.
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Affiliation(s)
- Pengfei Meng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Yanxin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Yumeng Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Tong Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Mingxia Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Yanbo Wang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and School of Marine Science, Ningbo University, Ningbo 315211, China; Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China.
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10
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Xu Q, Zheng L, Huang M, Zhao M. Collagen derived Gly-Pro-type DPP-IV inhibitory peptides: Structure-activity relationship, inhibition kinetics and inhibition mechanism. Food Chem 2024; 441:138370. [PMID: 38199113 DOI: 10.1016/j.foodchem.2024.138370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Our previous study has demonstrated that both the amino acid at N3 position and peptide length affected the DPP-IV inhibitory activity of Gly-Pro-type peptides. To further elucidate their molecular mechanism, a combined approach of QSAR modeling, enzymatic kinetics and molecular docking was used. Results showed that the QSAR models of Gly-Pro-type tripeptides and Gly-Pro-type peptides containing 3-12 residues were successfully constructed by 5z-scale descriptor with R2 of 0.830 and 0.797, respectively. The lower values of electrophilicity, polarity, and side-chain bulk of amino acid at N3 position caused higher DPP-IV inhibitory activity of Gly-Pro-type peptides. Moreover, an appropriate increase in the length of Gly-Pro-type peptides did not change their competitive inhibition mode, but decreased their inhibition constants (Ki values) and increased interactions with DPP-IV. More importantly, the interactions between the residues at C-terminal of Gly-Pro-type peptides containing 5 ∼ 6 residues with S2 extensive subsites (Ser209, Phe357, Arg358) of DPP-IV increased the interactions of Gly residue at N1 position with the S2 subsites (Glu205, Glu206, Asn710, Arg125, Tyr662) and decreased the acylation level of DPP-IV-peptide complex, and thereby increasing peptides' DPP-IV inhibitory activity.
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Affiliation(s)
- Qiongyao Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Lin Zheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China.
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Chaozhou Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Chaozhou, 521000, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Chaozhou Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Chaozhou, 521000, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China.
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11
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Zhang D, Ge X, Jiao Y, Liu Y. Quality analysis of steamed beef with black tea and the mechanism of action of main active ingredients of black tea on myofibrillar protein. Food Chem 2024; 441:137997. [PMID: 38183715 DOI: 10.1016/j.foodchem.2023.137997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 01/08/2024]
Abstract
In this study, we analyzed the tea polyphenol composition, volatile flavor composition and storage stability of steamed beef with black tea. The molecular docking and dynamics were used to elucidate the interaction mechanism between the active components of black tea and myofibrillar proteins. The highest content of caffeine (CAF) was found in black tea steamed beef products, followed by catechin (C), epicatechin gallate (ECG), epicatechin gallate (EGCG) and theaflavins (TF). Steamed beef with black tea showed low ΔE* value, low TBARS value, low carbonyl content as well as high sulfhydryl content during storage. The addition of C, CAF, ECG, EGCG and TF enhanced the oxidative stability of myofibrillar protein. In this study, the effects of active components of black tea on the oxidative stability of myofibrillar protein and their interactions were determined, which could provide a reference for the application of black tea and its active components in meat products. At the same time, it can provide new ideas for the development of new meat products.
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Affiliation(s)
- Duoduo Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, Shaanxi, China
| | - Xinyu Ge
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, Shaanxi, China
| | - Yang Jiao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, Shaanxi, China
| | - Yongfeng Liu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, Shaanxi, China.
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12
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Wang Y, Cui J, Jiang Y, Zhang S, Chen L, Ma Z, Yang D, Zhang Z, Huang X, Yang Y, Guo J, Lu Z, Li C. Jiawei Yanghe Decoction attenuate allergic airway inflammation by suppressing group 2 innate lymphoid cells responses. J Ethnopharmacol 2024; 326:117927. [PMID: 38373665 DOI: 10.1016/j.jep.2024.117927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Jiawei Yanghe Decoction (JWYHD) is modified Yanghe Decoction (YHD). YHD historically utilized as a potent medicinal solution for addressing chronic inflammatory conditions, holds promising therapeutic potential in the treatment of asthma. However, the mechanisms underlying JWYHD's effects on allergic asthma remain unclear. AIM OF THE STUDY To investigate the therapeutic effect as well as the underlying mechanisms of JWYHD on asthmatic mice. MATERIALS AND METHODS The ovalbumin (OVA)-induced mouse model was utilized, followed by the administration of JWYHD to allergic asthmatic mice. Subsequently, inflammatory cells in the bronchoalveolar lavage fluid (BALF) and lung tissues were conducted. The levels of various cytokines including interleukin (IL)-4, IL-5, IL-13, IL-33, tumor necrosis factor (TNF)-α, and interferon (IFN)-γ in BALF, as well as the total immunoglobulin E (IgE) content in serum, were assessed. Lung function and tissue pathology examinations were performed to assess the protective impacts of JWYHD. The chemical components of JWYHD and its lung prototype compounds (referred to the chemical components present in JWYHD that were observed in the lung) were explored by ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS). RNA-seq analysis revealed the regulation mechanisms of JWYHD treating asthma. Furthermore, the effect of JWYHD on type 2 innate lymphoid cells (ILC2s) in asthmatic mice was detected by flow cytometry and Smart-RNA-seq analysis. Then molecular docking analysis was used to show the interaction between identified compounds and key targets. RESULTS JWYHD significantly attenuated the airway inflammation of asthmatic mice, reduced the levels of inflammatory cells in BALF, as well the levels of the cytokines IL-4, IL-5, IL-13, IL-33, and TNF-α in BALF and IgE in serum. Airway hyperresponsiveness (AHR) and lung inflammation infiltration were also alleviated by JWYHD. Moreover, RNA-seq analysis revealed that JWYHD attenuated airway inflammation in asthmatic mice via regulating immunity. Flow cytometry confirmed that JWYHD could inhibit ILC2 responses. ILC2 Smart-RNA-seq analysis showed that JWYHD impaired the inflammation reaction-related signaling pathways in ILC2s, and neuropilin-1 (Nrp1), endothelial transcription factor 3 (GATA3) and interleukin 1 receptor like protein 1 (ST2) might be the key targets. The molecular docking analysis investigating the connection between the primary targets and JWYHD's prototype compounds in the lung demonstrated that liquiritin apioside, icariin, glycyrrhizic acid, and uralsaponin B, identified through UPLC-Q-TOF/MS, exhibited significant affinity in binding to the mentioned key targets. CONCLUSION Our results suggested that the mechanism of JWYHD in treating asthma might be related to limiting ILC2 responses. Our findings provided some pharmacological evidence for the clinical application of JWYHD in the treatment of asthma.
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Affiliation(s)
- Yu Wang
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Jie Cui
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Yuwei Jiang
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Shaoyan Zhang
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Linjin Chen
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Zifeng Ma
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Di Yang
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Zhengyi Zhang
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Xing Huang
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Yongqing Yang
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jinglei Guo
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhenhui Lu
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
| | - Cui Li
- Institute of Respiratory Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
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13
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Abid F, Saleem M, Jamshaid T, Jamshaid U, Youssef FS, Diri RM, Elhady SS, Ashour ML. Opuntia monacantha: Validation of the anti-inflammatory and anti-arthritic activity of its polyphenolic rich extract in silico and in vivo via assessment of pro- and anti-inflammatory cytokines. J Ethnopharmacol 2024; 326:117884. [PMID: 38350502 DOI: 10.1016/j.jep.2024.117884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/15/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Opuntia monacantha belongs to the cactus family Cactaceae and is also known by cochineal prickly pear, Barbary fig or drooping prickly pear. It was traditionally used to treat pain and inflammation. O. monacantha cladodes showed pharmacological effects such as antioxidant potential owing to the presence of certain polysaccharides, flavonoids, and phenols. AIM OF THE STUDY This research aimed to evaluate the anti-inflammatory as well as the anti-arthritic potential of ethanol extract of Opuntia monacantha (E-OM). MATERIALS AND METHODS In vivo edema in rat paw was triggered by carrageenan and used to evaluate anti-inflammatory activity, while induction of arthritis by Complete Freund's Adjuvant (CFA) rat model was done to measure anti-arthritic potential. In silico studies of the previously High performance liquid chromatography (HPLC) characterized metabolites of ethanol extract was performed by using Discovery Studio 4.5 (Accelrys Inc., San Diego, CA, USA) within active pocket of glutaminase 1 (GLS1) (PDB code: 3VP1; 2.30 Å). RESULTS EOM, particularly at 750 mg/kg, caused a reduction in the paw edema significantly and decreased arthritic score by 80.58% compared to the diseased group. It revealed significant results when histopathology of ankle joint was examined at 28th day as it reduced inflammation by 18.06%, bone erosion by 15.50%, and pannus formation by 24.65% with respect to the diseased group. It restored the altered blood parameters by 7.56%, 18.47%, and 3.37% for hemoglobin (Hb), white blood count (WBC), and platelets, respectively. It also reduced rheumatoid factor RF by 13.70% with concomitant amelioration in catalase (CAT) and superoxide dismutase (SOD) levels by 19%, and 34.16%, respectively, in comparison to the diseased group. It notably decreased mRNA expression levels of COX-2, IL-6, TNF-α, IL-1, NF-κβ and augmented the levels of IL-4 and IL-10 in real time PCR with respect to the diseased group and piroxicam. HPLC analysis previously performed showed that phenolic acids and flavonoids are present in E-OM. Molecular docking studies displayed pronounced inhibitory potential of these compounds towards glutaminase 1 (GLS1), approaching and even exceeding piroxicam. CONCLUSIONS Thus, Opuntia monacantha could be a promising agent to manage inflammation and arthritis and could be incorporated into pharmaceuticals.
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Affiliation(s)
- Farah Abid
- Department of Pharmacology, Faculty of Pharmacy, University of South Asia, Lahore, Pakistan.
| | - Mohammad Saleem
- Department of Pharmacology, Faculty of Pharmacy, University of the Punjab, Lahore, Pakistan.
| | - Talha Jamshaid
- Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
| | - Usama Jamshaid
- Faculty of Pharmacy, University of Strasbourg, Strasbourg, France.
| | - Fadia S Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo, 11566, Egypt.
| | - Reem M Diri
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Sameh S Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Mohamed L Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo, 11566, Egypt; Pharmacy Program, Department of Pharmaceutical Sciences, Batterjee Medical College, Jeddah, 21442, Saudi Arabia.
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14
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Gao Y, Yang Z, Ji T, Zhou P, Geng L, Gao X. Anti-papillary thyroid carcinoma effects of dioscorea bulbifera L. through ferroptosis and the PI3K/AKT pathway based on network pharmacology and experimental validation. J Ethnopharmacol 2024; 326:117912. [PMID: 38387682 DOI: 10.1016/j.jep.2024.117912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Papillary thyroid carcinoma (PTC) is the predominant form of thyroid cancer with a rising global incidence. Despite favorable prognoses, a significant recurrence rate persists. Dioscorea bulbifera L. (DBL), a traditional Chinese medicine, has been historically used for thyroid-related disorders. However, its therapeutic effects and mechanisms of action on PTC remain unclear. AIM OF THE STUDY To explore the potential therapeutic effects, principal active components, and molecular mechanisms of DBL in the treatment of PTC through network pharmacology and molecular docking, with experimental validation conducted to corroborate these findings. MATERIALS AND METHODS The Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) was utilized as a systematic tool for collecting and screening the phytochemical components of DBL, and for establishing associations between these components and molecular targets. Based on this, network data was visually processed using Cytoscape software (version 3.8.0). Concurrently, precise molecular docking studies of the principal active components of DBL and their corresponding targets were conducted using Autodock software. Additionally, PTC-related genes were selected through the GeneCards and GEO databases. We further employed the DAVID bioinformatics resources to conduct comprehensive Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses on the intersecting genes between DBL and PTC. These analyses aid in predicting the potential therapeutic actions of DBL on PTC and its mechanisms of action. To validate these findings, corresponding in vitro experimental studies were also conducted. RESULTS In this investigation, 14 bioactive compounds of DBL and 195 corresponding molecular targets were identified, with 127 common targets shared between DBL and PTC. Molecular docking revealed strong binding affinities between major bioactive compounds and target proteins. GO enrichment analysis unveiled key processes involved in DBL's action. KEGG analysis highlighted DBL's modulation of the PI3K/AKT signaling pathway. Experimental outcomes demonstrated DBL's potential in inhibiting PTC cell proliferation and migration, suppressing PI3K/AKT pathway activation, and promoting ferroptosis. CONCLUSION In conclusion, DBL offers a multifaceted therapeutic approach for PTC, targeting multiple molecular entities and influencing diverse biological pathways. Network pharmacology and molecular docking shed light on DBL's potential utility in PTC treatment, substantiated by experimental validation. This study contributes valuable insights into using DBL as a promising therapeutic agent for PTC management.
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Affiliation(s)
- Yuzhi Gao
- Department of Central Laboratory, Clinical College of Lianyungang, Bengbu Medical University, Lianyungang, 222002, Jiangsu, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Kangda College of Nanjing Medical University, Lianyungang 222002, Jiangsu, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Zhendong Yang
- Department of Ultrasonography, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Tuo Ji
- Department of Central Laboratory, Clinical College of Lianyungang, Bengbu Medical University, Lianyungang, 222002, Jiangsu, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Kangda College of Nanjing Medical University, Lianyungang 222002, Jiangsu, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Ping Zhou
- Endocrinology Department, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Lei Geng
- Department of Radiology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Xuzhu Gao
- Department of Central Laboratory, Clinical College of Lianyungang, Bengbu Medical University, Lianyungang, 222002, Jiangsu, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Kangda College of Nanjing Medical University, Lianyungang 222002, Jiangsu, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China.
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15
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Hu S, Wen J, Fan XD, Li P. Study on therapeutic mechanism of total salvianolic acids against myocardial ischemia-reperfusion injury based on network pharmacology, molecular docking, and experimental study. J Ethnopharmacol 2024; 326:117902. [PMID: 38360382 DOI: 10.1016/j.jep.2024.117902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/04/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Radix Salviae miltiorrhizae, also known as Danshen in Chinese, effectively activates the blood and resolves stasis. Total salvianolic acids (SA) is the main active ingredient of Danshen, and related preparations, such as salvianolate injection are commonly used clinically to treat myocardial ischemia-reperfusion injury (MIRI). However, the potential targets and key active ingredients of SA have not been sufficiently investigated. AIM OF THE STUDY This study aimed to investigate the mechanism of action of SA in treating MIRI. MATERIALS AND METHODS Network pharmacology and molecular docking techniques were used to predict SA targets against MIRI. The key acting pathway of SA were validated by performing experiments in a rat MIRI model. RESULTS Twenty potential ingredients and 54 targets of SA in treating MIRI were identified. Ingredient-target-pathway network analysis revealed that salvianolic acid B and rosmarinic acid had the highest degree value. Pathway enrichment analysis showed that SA may regulate MIRI through the IL-17 signaling pathway, and this result was confirmed in the rat MIRI experiment. CONCLUSION The results of this study indicate that SA may protect MIRI by regulating the IL-17 pathway.
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Affiliation(s)
- Shuang Hu
- Institute of Basic Medical Sciences, XiYuan Hospital of China Academy of Chinese Medical Sciences, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China; Key Laboratory of Pharmacology of Chinese Materia Medica of Beijing, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China; Graduate School of China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Jing Wen
- Institute of Basic Medical Sciences, XiYuan Hospital of China Academy of Chinese Medical Sciences, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China; Key Laboratory of Pharmacology of Chinese Materia Medica of Beijing, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China; Graduate School of China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Xiao-di Fan
- Institute of Basic Medical Sciences, XiYuan Hospital of China Academy of Chinese Medical Sciences, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China; Key Laboratory of Pharmacology of Chinese Materia Medica of Beijing, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China.
| | - Peng Li
- Institute of Basic Medical Sciences, XiYuan Hospital of China Academy of Chinese Medical Sciences, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China; Key Laboratory of Pharmacology of Chinese Materia Medica of Beijing, No.1 XiYuan CaoChang, Haidian District, Beijing, 100091, China.
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16
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Jiang Y, Yang L, Chen H, Chen J, Yang L, Wang Z, Yuan X, Shan J, Lin L, Li H, Ye J. Network pharmacology combined with lipidomics to reveal the regulatory effects and mechanisms of Kangzao granules in the hypothalamus of rats with central precocious puberty. J Pharm Biomed Anal 2024; 242:116059. [PMID: 38422672 DOI: 10.1016/j.jpba.2024.116059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Central precocious puberty (CPP) is a prevalent endocrine disorder that primarily affects children, specifically females, and is associated with various physical and psychological complications. Although Kangzao granules (KZG) are efficacious in managing CPP, the underlying mechanisms remain unclear. Therefore, this study aimed to elucidate the therapeutic mechanisms of KZG using network pharmacology, molecular docking, pharmacodynamics, and pathway validation. A putative compound-target-pathway network was constructed using Cytoscape, before KEGG and Gene Ontology enrichment analyses were conducted. Moreover, molecular docking was performed using AutoDockTools. Quality control of the 10 key components of KZG was carried out using UHPLC-ESI/LTQ-Orbitrap-MS/MS, and hypothalamic lipids were analyzed using UHPLC-Q-Exactive Orbitrap MS/MS. In total, 87 bioactive compounds that targeting 110 core proteins to alleviate CPP were identified in KZG. Lipidomic analysis revealed 18 differential lipids among the CPP, KZG, and control groups, wherein fatty acids were significantly reduced in the model group; however, these changes were effectively counteracted by KZG treatment. Molecular docking analysis revealed a strong binding affinity between flavonoids and RAC-alpha serine/threonine-protein kinase (AKT) when docked into the crystal structure. Moreover, a substantial disruption in lipid metabolism was observed in the model group; however, treatment with KZG efficiently reversed these alterations. Furthermore, the phosphoinositide 3-kinase/AKT signaling pathway was identified as a pivotal regulator of hypothalamic lipid metabolism regulator. Overall, this study highlights the effectiveness of a multidisciplinary approach that combines network pharmacology, lipidomics, molecular docking, and experimental validation in the elucidation of the therapeutic mechanisms of KZG in CPP treatment.
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Affiliation(s)
- Yanhua Jiang
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China; Department of Pediatrics, Shaoxing Hospital of Traditional Chinese Medicine, Shaoxing, China
| | - Lixia Yang
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Chen
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiabin Chen
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Lingling Yang
- Department of Pediatric, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, China
| | - Zhao Wang
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Xuejing Yuan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Lili Lin
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Hui Li
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Jin Ye
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
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17
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Igbokwe CJ, Feng Y, Louis H, Benjamin I, Quaisie J, Duan Y, Tuly JA, Cai M, Zhang H. Novel antioxidant peptides identified from coix seed by molecular docking, quantum chemical calculations and invitro study in HepG2 cells. Food Chem 2024; 440:138234. [PMID: 38145582 DOI: 10.1016/j.foodchem.2023.138234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
The aim of the study was to identify potent antioxidant peptides sourced from coix seed, analyze the structure-activity relationship through molecular docking and quantum chemical calculation. Molecular docking results showed that among thirteen peptides selected in silico, eight had favourable binding interaction with the Keap1-Kelch domain (2FLU). Promising peptides with significant binding scores were further evaluated using quantum calculation. It was shown that peptide FFDR exhibited exceptional stability, with a high energy gap of 5.24 eV and low Highest Occupied Molecular Orbitals (HOMO) and Lowest Unoccupied Molecular Orbitals (LUMO) values. Furthermore, FFDR displayed the capacity to enhance the expression of Nrf2-Keap1 antioxidant genes (CAT, SOD, GSH-Px) and improved cellular redox balance by increasing reduced glutathione (GSH) while reducing oxidized glutathione (GSSG) and malonaldehyde (MDA) levels. These findings highlight the potential of coix seed peptides in developing novel, effective and stable antioxidant-based functional foods.
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Affiliation(s)
- Chidimma Juliet Igbokwe
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China; Department of Food Science and Technology, University of Nigeria Nsukka, Nigeria
| | - Yuqin Feng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria; School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Innocent Benjamin
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Janet Quaisie
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China; Chemistry and Nutrition Research Division, Food Research Institute, Accra, Ghana
| | - Yuqing Duan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China; Institute of Food Physical Processing, Jiangsu University, Zhenjiang 212013, China.
| | - Jamila A Tuly
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Meihong Cai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Haihua Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China.
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Gao J, Wang N, Song W, Yuan Y, Teng Y, Liu Z. Mechanisms underlying the synergistic effects of chuanxiong combined with Chishao on treating acute lung injury based on network pharmacology and molecular docking combined with preclinical evaluation. J Ethnopharmacol 2024; 325:117862. [PMID: 38342157 DOI: 10.1016/j.jep.2024.117862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 02/13/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The herb pair of Chuanxiong Rhizome (Ligusticum chuanxiong Hort., Chuanxiong in Chinese, CX) and Paeoniae Radix Rubra (Paeonia lactiflora Pall. Or Paeonia veitchii Lynch, Chishao in Chinese, CS) is a famous blood activating and stasis resolving pair that is often found in traditional Chinese medicine (TCM) formulas for the treatment of acute lung injury (ALI). However, the relationship of CX-CS herb pair to ALI and its underlying mechanisms are unclear. AIM OF THE STUDY The study explored the effect and mechanisms of CX-CS herb pair in LPS induced ALI by network pharmacology and molecular docking combined with preclinical evaluation. MATERIALS AND METHODS The related targets of the active compounds of CX-CS herb pair in regulating ALI were screened by network pharmacology. PPI was constructed and the potential pathways were investigated by GO and KEGG. The contribution of each active ingredient of CX-CS herb pair to ALI were calculated by network-based efficacy. The interactions between potential targets and active ingredients were evaluated by molecular docking. LPS stimulated RAW264.7 cells and mice model experiments were adopted to verify the effect of CX-CS herb pair on ALI. RESULTS A total of 25 compounds and 193 targets were identified in the CX-CS herb pair, of which 19 compounds and 64 targets were associated with ALI, and six compounds including baicalin, ellagic acid, baicalein, beta-sitosterol, paeoniflorin and ferulic acid accounted for 93.12% of the total combination index for ALI prevention. The CX-CS herbal pair against ALI was associated with PI3K/AKT and MAPK signaling pathways by GO and KEGG analysis. The screened active compounds showed good affinity for TNF, MAPK, and AKT by molecular docking. In vitro and in vivo tests showed that CX combined with CS synergistically inhibited LPS-induced ALI at 1:3, suppressed the release of TNF-α, IL-1β and IL-6, inhibited the accumulation of ROS, as well as regulated the content of SOD, MDA and GSH. Meanwhile, the herb pair was effective in inhibiting the expression of p38, ERK, IκBα, p65, caspase 3, PARP, and up-regulating the levels of AKT and Bcl-2/Bax. CONCLUSIONS Our study confirmed the synergistic effect of CX-CS herb pair on the prevention of ALI by inhibiting inflammation, oxidative stress, and apoptosis through MAPK/NF-κB and PI3K/AKT signaling pathways.
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Affiliation(s)
- Junling Gao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ning Wang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Wenjuan Song
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yajie Yuan
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yuou Teng
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Zhen Liu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
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19
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Zhao Q, Fan Y, Zhao L, Zhu Y, Jiang Y, Gu J, Xue Y, Hao Z, Shen Q. Identification and molecular binding mechanism of novel pancreatic lipase and cholesterol esterase inhibitory peptides from heat-treated adzuki bean protein hydrolysates. Food Chem 2024; 439:138129. [PMID: 38100876 DOI: 10.1016/j.foodchem.2023.138129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Heat-treated adzuki bean protein hydrolysates exhibit lipid-reducing properties; however, few studies have reported pancreatic lipase (PL) and cholesterol esterase (CE) inhibitory effects and elucidated the underlying mechanisms. In this study, we accomplished the identification of antiobesity peptides through peptide sequencing, virtual screening, and in vitro experiments. Furthermore, the mechanisms were investigated via molecular docking. The findings reveal that the action of pepsin and pancreatin resulted in the transformation of intact adzuki bean protein into smaller peptide fragments. The < 3 kDa fraction exhibited a high proportion of hydrophobic amino acids and displayed superior inhibitory properties for both PL and CE. Five novel antiobesity peptides (LLGGLDSSLLPH, FDTGSSFYNKPAG, IWVGGSGMDM, YLQGFGKNIL, and IFNNDPNNHP) were identified as PL and CE inhibitors. Particularly, IFNNDPNNHP exhibited the most robust biological activity. These peptides exerted their inhibitory action on PL and CE by occupying catalytic or substrate-binding sites through hydrogen bonds, hydrophobic interactions, salt bridges, and π-π stacking.
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Affiliation(s)
- Qingyu Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, Beijing 100083, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yimeng Fan
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Liangxing Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, Beijing 100083, China
| | - Yiqing Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, Beijing 100083, China
| | - Yuanrong Jiang
- Wilmar (Shanghai) Biotechnology Research & Development Center Co., Ltd, Shanghai 200137
| | - Jie Gu
- Wilmar (Shanghai) Biotechnology Research & Development Center Co., Ltd, Shanghai 200137
| | - Yong Xue
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, Beijing 100083, China
| | - Zhihui Hao
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qun Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, Beijing 100083, China.
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20
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Luo H, Wang Z. Pan-cancer analysis reveals potential immunological and prognostic roles of COA6 in human cancers and preliminary exploration of COA6 in bladder cancer. Cell Signal 2024; 117:111111. [PMID: 38395184 DOI: 10.1016/j.cellsig.2024.111111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Cytochrome C oxidase assembly factor 6 (COA6) is significantly involved in the progression of cancer and is aberrantly expressed in disease. Nevertheless, the comprehensive analysis of COA6 using many omics techniques, and its impact on the prognosis and immunological microenvironment of cancer patients, remains unexplored. METHODS We gathered data from 33 cancer cases and conducted a thorough analysis of abnormalities in COA6 gene expression. This analysis included examining its relevance to disease, its diagnostic and prognostic value, pathway enrichment, the immune microenvironment, its association with immune checkpoints, and its ability to predict patient response to immunotherapy and natural small molecule drugs that target the COA6 protein. Ultimately, we examined the function of COA6 in bladder cancer by in vitro research. RESULTS Our study revealed significant variations in gene expression and identified COA6 as a potential diagnostic biomarker for cancer. COA6 was also discovered to have a crucial function in pan-cancer involving the tumor microenvironment. COA6 has a strong correlation with well-known immunological checkpoints, including TMB and MSI. Molecular docking identified natural small chemical inhibitors that specifically target the COA6 protein. Ultimately, scientific evidence has verified that suppressing the expression of the COA6 gene hinders the growth and infiltration of bladder cancer cells. CONCLUSIONS Our study emphasizes the significant potential of COA6 as a predictive and immunotherapeutic response biomarker. This finding may lead to future investigation into the mechanism of tumor infiltration and the therapeutic possibilities of COA6 in cancer.
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Affiliation(s)
- Hong Luo
- Department of Oncology, Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng 224001, Jiangsu Province, China
| | - Zhiyong Wang
- Gastrointestinal Surgery, Wuhan Union Hospital, Wuhan 430022, Hubei, China.
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21
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Sun Z, Liang C, Ling Y, Chen Y, Ma Z, Xu Y, Liu Z. A study on the subchronic toxicity of triclocarban to the early-life development of oryzias melastigma and focused on the analysis of osmoregulatory regulation mechanisms. Comp Biochem Physiol C Toxicol Pharmacol 2024; 279:109882. [PMID: 38437996 DOI: 10.1016/j.cbpc.2024.109882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/27/2024] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
Triclocarban (TCC), a novel antimicrobial agent found in personal care products, has been extensively detected in marine environments. However, research on the toxic effects of TCC on marine organisms remains inadequate. This study delved into the subchronic toxic effects of TCC on the early life stages of marine medaka (Oryzias melastigma, O. melastigma), revealing that TCC could reduce embryo heart rate and hatching rate while diminishing the survival rate of larvae. Biomarker assays indicated that TCC could inflict damage on the embryos' antioxidant and nervous systems. Transcriptomic analysis suggested that TCC could impact cell growth, reproduction, and various life processes, activating cancer signaling pathways, increasing the likelihood of cancer, and exerting toxic effects on the immune and osmoregulatory systems. To validate and enhance our understanding of TCC's unique toxic impact on the osmoregulatory system of O. melastigma, we conducted homology modeling and molecular docking analyses on the protein involved in osmoregulation. The study intuitively revealed the potential binding affinity of TCC to sodium/potassium-transporting ATPase subunit alph (ATP1A1), indicating its ability to disrupt osmotic balance in marine fish by affecting this target protein. In summary, the results of this study will further enhance our comprehension of the potential toxic effects and mechanisms of TCC on the early stages of marine fish, with a specific focus on its unique toxic effects in osmoregulation.
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Affiliation(s)
- Zhecheng Sun
- School of Environmental Science and Engineering, Nanjing tech university, Nanjing 211816, China
| | - Chuan Liang
- School of Environmental Science and Engineering, Nanjing tech university, Nanjing 211816, China
| | - Yunzhe Ling
- School of Environmental Science and Engineering, Nanjing tech university, Nanjing 211816, China
| | - Yang Chen
- School of Environmental Science and Engineering, Nanjing tech university, Nanjing 211816, China
| | - Zhengzhuo Ma
- School of Environmental Science and Engineering, Nanjing tech university, Nanjing 211816, China
| | - Yanhua Xu
- School of Environmental Science and Engineering, Nanjing tech university, Nanjing 211816, China
| | - Zhiying Liu
- School of Environmental Science and Engineering, Nanjing tech university, Nanjing 211816, China.
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22
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Lu ZJ, Shi WJ, Ma DD, Zhang JG, Long XB, Li SY, Gao FZ, Zhang QQ, Ying GG. The azole biocide climbazole induces oxidative stress, inflammation, and apoptosis in fish gut. Sci Total Environ 2024; 923:171475. [PMID: 38453063 DOI: 10.1016/j.scitotenv.2024.171475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
Climbazole is an azole biocide that has been widely used in formulations of personal care products. Climbazole can cause developmental toxicity and endocrine disruption as well as gut disturbance in aquatic organisms. However, the mechanisms behind gut toxicity induced by climbazole still remain largely unclear in fish. Here, we evaluate the gut effects by exposing grass carp (Ctenopharyngodon idella) to climbazole at levels ranging from 0.2 to 20 μg/L for 42 days by evaluating gene transcription and expression, biochemical analyses, correlation network analysis, and molecular docking. Results showed that climbazole exposure increased cyp1a mRNA expression and ROS level in the three treatment groups. Climbazole also inhibited Nrf2 and Keap1 transcripts as well as proteins, and suppressed the transcript levels of their subordinate antioxidant molecules (cat, sod, and ho-1), increasing oxidative stress. Additionally, climbazole enhanced NF-κB and iκBα transcripts and proteins, and the transcripts of NF-κB downstream pro-inflammatory factors (tnfα, and il-1β/6/8), leading to inflammation. Climbazole increased pro-apoptosis-related genes (fadd, bad1, and caspase3), and decreased anti-apoptosis-associated genes (bcl2, and bcl-xl), suggesting a direct reaction to apoptosis. The molecular docking data showed that climbazole could form stable hydrogen bonds with CYP1A. Mechanistically, our findings suggested that climbazole can induce inflammation and oxidative stress through CYP450s/ROS/Nrf2/NF-κB pathways, resulting in cell apoptosis in the gut of grass carp.
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Affiliation(s)
- Zhi-Jie Lu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Wen-Jun Shi
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Dong-Dong Ma
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jin-Ge Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Xiao-Bing Long
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Si-Ying Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Qian-Qian Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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23
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Xiang X, Yang Q, Chen K, Wang Z, Yang G, Li A, An X, Kan J. Characterization of key bitter compounds in Idesia polycarpa var. vestita Diels fruit by sensory-guided fractionation. Food Chem 2024; 439:138103. [PMID: 38056337 DOI: 10.1016/j.foodchem.2023.138103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/14/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023]
Abstract
Idesia polycarpa var. vestita Diels (I. vestita) has become a promising oil crop due to its easily digestible and highly nutritious fruit oil. However, the intense bitter taste of its fruit greatly limits its development and promotion in the food industry. Herein, five key bitter compounds from I. vestita fruit were isolated by sensory-guided fractionation and characterized using ultra-high performance liquid chromatography-quadrupole time of flight-mass spectrometer and nuclear magnetic resonance. The bitter taste of the identified compounds was subsequently validated by threshold tests and computational molecular docking. The bitterness threshold in water of idesin was the lowest (12.051 mg/L), and all bitter substances spontaneously bound to the bitter receptors hTAS2R16 and hTAS2R14, with a stronger affinity for the latter (approximately -6.5 - -9.0 kcal/mol). This is the first systematic study of bitter compounds in I. vestita fruit, providing a scientific basis for revealing the mechanism of bitterness formation and bitterness control.
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Affiliation(s)
- Xuwen Xiang
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Chongqing 400715, PR China
| | - Qingqing Yang
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Chongqing 400715, PR China
| | - Kewei Chen
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Chongqing 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China
| | - Zhirong Wang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, PR China
| | - Gang Yang
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Chongqing 400715, PR China
| | - Aijun Li
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Chongqing 400715, PR China
| | - Xiaofeng An
- Chongqing Shanlinyuan Forestry Comprehensive Development Co., Ltd., Chongqing 400800, PR China
| | - Jianquan Kan
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Chongqing 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China.
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24
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Oza Y, Patel R, Patel D, Shukla A. Taming Pseudomonas aeruginosa AM26 the barbarian: Targeting the PQS quorum sensing network using crude mandarin extract. Diagn Microbiol Infect Dis 2024; 109:116212. [PMID: 38387214 DOI: 10.1016/j.diagmicrobio.2024.116212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Pseudomonas aeruginosa, one of the most notorious organisms, causes fatal diseases like-, meningitis, pneumonia as well as worsens the prognosis of cystic fibrosis patients. It is also multi-drug resistant and resists a wide range of antibiotics. Attempts have been made to reduce its virulence/pathogenic potential using a number of organic compounds. For this purpose, the Quorum sensing (QS) system of P. aeruginosa was targeted, which regulates its virulence. Pseudomonas Quinolone System (PQS), one of the four quorum sensing systems, producing pyocyanin pigment was chosen. 2-heptyl-3-hydroxy-4-quinolone (HHQ) is a ligand which binds to PQS protein is responsible for pyocyanin pigment production. Attempts were made to find a compound analogous to HHQ which could bind to PQS active site and inhibit the pigment formation. In-silico analysis was performed to estimate possible interactions and to find/predict the possible PQS inhibitors.
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Affiliation(s)
- Yukti Oza
- National Centre for Cell Science, Pune Savitribai Phule Pune University Campus Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Rohit Patel
- Department of Microbiology and Biotechnology, Gujarat University, Navrangpura, Ahmedabad, 380009, Gujarat, India
| | - Dhara Patel
- Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, 382426, Gujarat, India
| | - Arpit Shukla
- Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, 382426, Gujarat, India.
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25
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Guan P, Fan S, Dong W, Wang X, Li Z, Song M, Suo B. Comparative genomic analysis and multilocus sequence typing of Staphylococcus aureus reveals candidate genes for low-temperature tolerance. Sci Total Environ 2024; 923:171331. [PMID: 38428609 DOI: 10.1016/j.scitotenv.2024.171331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types. The ST352 strains exhibited the greatest tolerance to low temperature, with a mean reduction in survival rate of 10.34 % (p < 0.05). Comparative genomics revealed a total of 1941 core genes in the three S. aureus strains, and BB-1 had 468 specific genes, which were enriched mainly in translation, DNA recombination, DNA repair, metabolic pathways, two-component systems, and quorum sensing. Molecular docking analysis revealed that the binding of the RsbW protein to the SigB protein of BB-1 decreased due to base mutations in rsbW, while the binding to the RsbV protein was enhanced. In addition, the results of real-time quantitative PCR showed that the RsbV-RsbW/SigB system of BB-1 may play a role in the low-temperature survival of S. aureus and the formation of SCVs. These results suggest that genes specific to BB-1 may contribute to the mechanism of adaptation to low temperature and the formation of SCVs. This study helps elucidate the causes of SCV formation by S. aureus at low temperature at the molecular level and provides a basis for exploring the safety control of cold chain food environments.
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Affiliation(s)
- Peng Guan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Shijia Fan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Wenjing Dong
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xiaojie Wang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Zhen Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Miao Song
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Biao Suo
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China.
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Sandhya KS, Kishore AA, Unni A, Sunitha P, Sajithra CV, Nair AS. Interaction analysis of SARS-CoV-2 omicron BA1 and BA2 of RBD with fifty monoclonal antibodies: Molecular dynamics approach. J Mol Graph Model 2024; 128:108719. [PMID: 38324968 DOI: 10.1016/j.jmgm.2024.108719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
This report provides detailed insights into the interaction of fifty monoclonal antibodies with two recent Omicron variants, BA1 and BA2. It has been observed that numerous mutations in the receptor binding domain (RBD) result in significant structural changes in Omicron, enhancing its ability to mediate viral infections compared to other variants of concern. The following antibodies, namely JX3S304, 7KMG, 7CH4, 7BELCOVOX45, 7CDJ, 7C01, 7JX3S2H14, 6XCA, 7CDI, 7JMO, 7B3O, 6ZER, 6XC7CR3022, JX3S309, 6XC7CC123, 7CM4, 7KMI, 7L7EAZD8895, exhibit a superior binding affinity towards the Spike when compared to the reference CR3022. Four best-docked systems were subjected to further testing through molecular dynamics (MD) simulations. The MM/GBSA free energy for the top-scored complexes of BA1 variant are BA1_JX3S3O4, BA1_7KMI, BA1_7CH4, and BA1_7KMG, with respective values of -56.120 kcal/mol, -41.30 kcal/mol, -17.546 kcal/mol, and -8.527 kcal/mol; and of BA2 variant are BA2_JX3S3O4, BA2_7CM4, BA2_KMG, and BA2_7CH4, with respective values of -40.903 kcal/mol, -23.416 kcal/mol, -17.350 kcal/mol, and -5.460 kcal/mol. Detailed structural/energetic parameters, principal component analysis, and free energy landscape (FEL) studies reveal a significant decrease in antibody resistance due to the disappearance of numerous hydrogen bond interactions and various metastable states. We believe that these crucial mechanistic insights will contribute to breakthroughs in SARS-CoV-2 research.
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Affiliation(s)
- K S Sandhya
- Department of Computational Biology and Bioinformatics, University of Kerala, India; Department of Chemistry, University of Kerala, Kerala, India.
| | | | - Arun Unni
- Department of Computational Biology and Bioinformatics, University of Kerala, India
| | - P Sunitha
- Department of Computational Biology and Bioinformatics, University of Kerala, India
| | - C V Sajithra
- Department of Chemistry, University of Kerala, Kerala, India
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, India
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Huang F, Dai Q, Zheng K, Ma Q, Liu Y, Jiang S, Jiang W, Yan X. Exploring the inhibitory potential of KPHs-AL-derived GLLF peptide on pancreatic lipase and cholesterol esterase activities. Food Chem 2024; 439:138108. [PMID: 38061297 DOI: 10.1016/j.foodchem.2023.138108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 01/10/2024]
Abstract
The effective modulation of pancreatic lipase and cholesterol esterase activities proves critical in maintaining circulatory triglycerides and cholesterol levels within physiological boundaries. In this study, peptides derived from KPHs-AL, produced through the enzymatic hydrolysis of skipjack tuna dark muscle using alkaline protease, have a specific inhibitory effect on pancreatic lipase and cholesterol esterase. It is hypothesized that these peptides target and modulate the activities of enzymes by inducing conformational changes within their binding pockets, potentially impacting the catalytic functions of both pancreatic lipase and cholesterol esterase. Results revealed these peptides including AINDPFIDL, FLGM, GLLF and WGPL, were found to nestle into the binding site groove of pancreatic lipase and cholesterol esterase. Among these, GLLF stood out, demonstrating potent inhibition with IC50 values of 0.1891 mg/mL and 0.2534 mg/mL for pancreatic lipase and cholesterol esterase, respectively. The kinetics studies suggested that GLLF competed effectively with substrates for the enzyme active sites. Spectroscopic analyses, including ultraviolet-visible, fluorescence quenching, and circular dichroism, indicated that GLLF binding induced conformational changes within the enzymes, likely through hydrogen bond formation and hydrophobic interactions, thereby increasing structural flexibility. Molecular docking and molecular dynamics simulations supported these findings, showing GLLF's stable interaction with vital active site residues. These findings position GLLF as a potent inhibitor of key digestive enzymes, offering insights into its role in regulating lipid metabolism and highlighting its potential as functional ingredient.
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Affiliation(s)
- Fangfang Huang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China; Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Qingfei Dai
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Kewei Zheng
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Qingbao Ma
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Yu Liu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Shuoqi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi, Jiangsu, China
| | - Wei Jiang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China.
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
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Xu Y, Cao S, Wang SF, Ma W, Gou XJ. Zhisou powder suppresses airway inflammation in LPS and CS-induced post-infectious cough model mice via TRPA1/TRPV1 channels. J Ethnopharmacol 2024; 324:117741. [PMID: 38224794 DOI: 10.1016/j.jep.2024.117741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Zhisou Powder (ZSP), a traditional Chinese medicine (TCM) prescription, has been widely used in the clinic for the treatment of post-infectious cough (PIC). However, the exact mechanism is not clear. AIM OF THE STUDY The aim of this study was to investigate the ameliorative effect of ZSP on PIC in mice. The possible mechanisms of action were screened based on network pharmacology, and the potential mechanisms were explored through molecular docking and in vivo experimental validation. MATERIALS AND METHODS Lipopolysaccharide (LPS) (80μg/50 μL) was used to induce PIC in mice, followed by daily exposure to cigarette smoke (CS) for 30 min for 30 d to establish PIC model. The effects of ZSP on PIC mice were observed by detecting the number of coughs and cough latency, peripheral blood and bronchoalveolar lavage fluid (BALF) inflammatory cell counts, enzyme-linked immunosorbent assay (ELISA), and histological analysis. The core targets and key pathways of ZSP on PIC were analyzed using network pharmacology, and TRPA1 and TRPV1 were validated using RT-qPCR and western blotting assays. RESULTS ZSP effectively reduced the number of coughs and prolonged the cough latency in PIC mice. Airway inflammation was alleviated by reducing the expression levels of the inflammatory mediators TNF-α and IL-1β. ZSP modulated the expression of Substance P, Calcitonin gene-related peptide (CGRP), and nerve growth factor (NGF) in BALF. Based on the results of network pharmacology, the mechanism of action of ZSP may exert anti-neurogenic airway-derived inflammation by regulating the expression of TRPA1 and TRPV1 through the natural active ingredients α-spinastero, shionone and didehydrotuberostemonine. CONCLUSION ZSP exerts anti-airway inflammatory effects through inhibition of TRPA1/TRPV1 channels regulating neuropeptides to alleviate cough hypersensitivity and has a favorable therapeutic effect on PIC model mice. It provides theoretical evidence for the clinical application of ZSP.
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Affiliation(s)
- Yuan Xu
- Respiratory Department and Central Laboratory, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine of Shanghai, Shanghai 201999, China; School of Pharmacy, Shaanxi Univesity of Chinese Medicine, Shaanxi, Xianyang 712046, China
| | - Shan Cao
- Respiratory Department and Central Laboratory, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine of Shanghai, Shanghai 201999, China
| | - Shu-Fei Wang
- School of Pharmacy, Shaanxi Univesity of Chinese Medicine, Shaanxi, Xianyang 712046, China
| | - Wei Ma
- Respiratory Department and Central Laboratory, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine of Shanghai, Shanghai 201999, China.
| | - Xiao-Jun Gou
- Respiratory Department and Central Laboratory, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine of Shanghai, Shanghai 201999, China.
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Kong J, Xiang Q, Ge W, Wang Y, Xu F, Shi G. Network pharmacology mechanisms and experimental verification of licorice in the treatment of ulcerative colitis. J Ethnopharmacol 2024; 324:117691. [PMID: 38176667 DOI: 10.1016/j.jep.2023.117691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/10/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Licorice is widely used in the treatment of ulcerative colitis (UC) and has good antioxidant and anti-inflammatory effects, but its specific active ingredients and mechanisms of action are still unknown. THE PURPOSE OF THE STUDY To elucidate the specific molecular mechanisms of licorice in the treatment of UC and to experimentally verify its activity. METHODS Through network pharmacology, the active ingredients of licorice and the molecular targets of UC were identified. A traditional Chinese medicine (TCM)-components-target-disease network diagram was established, and the binding energies of the active ingredient and targets of licorice were verified by molecular docking. A BALB/c mice model of UC was established by treatment with 3% dextran sulfate sodium (DSS). The effect of licorice on colon tissue injury was histologically assessed. The expression of IL-6 and IL-17 in colon tissue was detected by immunohistochemistry (IHC). Transmission electron microscopy (TEM) was used to observe morphological changes in mitochondria in the colon. Caco2 cells were treated with lipopolysaccharide (LPS) for 24 h to establish the cell inflammatory damage model, and cells were exposed to different concentrations of drug-containing serum of Licorice (DCSL) for 24 h. In cells treated with the drug, the contents of oxidation markers were measured and ELISA was used to determine the levels of inflammatory factors in the cells. TEM was used to observe morphological changes in mitochondria. ZO-1 and occludin were detected by Western blotting. DCSL effects on autophagy were evaluated by treating cells with DCSL and autophagy inhibitor for 24 h after LPS injection. Small interfering ribonucleic acid (si-RNA) was used to silence Nrf2 gene expression in Caco2 cells to observe the effects of DCSL on autophagy through the Nrf2/PINK1 pathway. Nrf2, PINK1, HO-1, Parkin, P62, and LC3 were detected by Western blotting. RESULTS Ninety-one active ingredients and 339 action targets and 792 UC disease targets were identified, 99 of which were overlapping targets. Molecular docking was used to analyze the binding energies of liquiritin, liquiritigenin, glycyrrhizic acid, and glycyrrhetinic acid to the targets, with glycyrrhetinic acid having the strongest binding energy. In the UC mouse model, licorice improved colon histopathological changes, reduced levels of IL-6 and IL-17 and repaired mitochondrial damage. In the LPS-induced inflammation model of Caco2 cells, DCSL decreased MDA, IL-1β, Il-6, and TNF-α levels and increased those of Superoxide Dismutase (SOD), glutathione peroxidase (GSH-PX), and IL-10, and improved the morphological changes of mitochondria. Increased expression of Nrf2, PINK1, Parkin, HO-1, ZO-1, occludin, P62, and LC3 promoted autophagy and reduced inflammation levels. CONCLUSION Licorice improves UC, which may be related to the activation of the Nrf2/PINK1 signaling pathway that regulates autophagy.
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Affiliation(s)
- Jinrong Kong
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei City, Anhui Province, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei City, Anhui Province, China
| | - Qingzhen Xiang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei City, Anhui Province, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei City, Anhui Province, China
| | - Wanyue Ge
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei City, Anhui Province, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei City, Anhui Province, China
| | - Yunlai Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei City, Anhui Province, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei City, Anhui Province, China
| | - Fan Xu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei City, Anhui Province, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei City, Anhui Province, China.
| | - Gaoxiang Shi
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei City, Anhui Province, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei City, Anhui Province, China.
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Liu T, Zhuang XX, Tang YY, Gao YC, Gao JR. Mechanistic insights into Qiteng Xiaozhuo Granules' regulation of autophagy for chronic glomerulonephritis treatment: Serum pharmacochemistry, network pharmacology, and experimental validation. J Ethnopharmacol 2024; 324:117819. [PMID: 38286158 DOI: 10.1016/j.jep.2024.117819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/13/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Qiteng Xiaozhuo Granules (QTXZG), a traditional Chinese medicine prescription, is widely acknowledged for its therapeutic efficacy and lack of discernible toxicity in clinical practice, substantiating its potential in the treatment of chronic glomerulonephritis (CGN). Nevertheless, the specific effectiveness and underlying mechanisms of QTXZG remain insufficiently explored. AIM OF THE STUDY The purpose of this study was to explore the mechanism of the QTXZG in the treatment of CGN via targeting autophagy based on serum pharmacochemistry, network pharmacology, and experimental validation. METHODS Serum samples from SD rats orally administered QTXZG were analyzed using UPLC-QE/MS to identify contained compounds. Network and functional enrichment analyses elucidated QTXZG's targets and biological mechanisms. Reliability was ensured through molecular docking, in vivo and in vitro experiments. RESULTS After oral administration of QTXZG, 39 enriched compounds in serum samples collected 1 h later were identified as potential active agents, with 508 potential targets recognized as QTXZG-specific targets. Through integration of various databases, intersection analysis of QTXZG targets, CGN-related genes, and autophagy-related targets identified 10 core autophagy-related targets for QTXZG in CGN. GO and KEGG analyses emphasized their roles in autophagy, inflammation, and immune processes, particularly emphasizing the enrichment of the AMPK/mTOR signaling pathway. Molecular docking results demonstrated strong binding affinities between QTXZG's key compounds and the predicted core targets. In animal experiments, QTXZG was found to ameliorate renal tissue damage in CGN model mice, significantly reducing serum creatinine (Scr) and blood urea nitrogen (BUN) levels. Importantly, both animal and cell experiments revealed QTXZG's ability to decrease excessive ROS and inflammatory factor release in mesangial cells. Furthermore, in vitro and in vivo experiments confirmed QTXZG's capacity to upregulate Beclin1 and LC3II/I expression, decrease p62 expression, and induce CGN autophagy through modulation of the AMPK/mTOR pathway. CONCLUSIONS This study indicated that QTXZG can induce autophagy in CGN by affecting the AMPK/mTOR pathway, and induction of autophagy may be one of the possible mechanisms of QTXZG's anti-CGN.
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Affiliation(s)
- Tao Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China; College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230011, Anhui, China.
| | - Xing Xing Zhuang
- Department of Pharmacy, Chaohu Hospital of Anhui Medical University, Chaohu, 238000, Anhui, China.
| | - Yong Yan Tang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China; College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230011, Anhui, China.
| | - Ya Chen Gao
- Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.
| | - Jia Rong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.
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Xiang P, Li Q, Cui G, Xu N, Xiao Q, Qu X, Zhang Y, Chen Y, Wei X, Wang Q, Zhong R, Liu K, Liu C, Zhu F. Investigating the mechanism and efficacy material basis of Xiehuo Xiaoying decoction for treating Graves' disease via thyroid cell apoptosis based on proteomics and molecular docking techniques. J Ethnopharmacol 2024; 324:117753. [PMID: 38218499 DOI: 10.1016/j.jep.2024.117753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE For numerous years, the Xiehuo Xiaoying decoction (XHXY), a traditional Chinese medicine formula, has demonstrated substantial promise in treating Graves' disease (GD) in clinical settings, showcasing significant potential. However, the therapeutic mechanism and efficacy material basis of XHXY remains obscure. AIM OF THE STUDY This work aims to investigate the underlying mechanisms and to study the efficacy material basis of XHXY in anti-GD effect using a combination of TMT quantitative proteomics and molecular docking method. MATERIALS AND METHODS GD model was initiated by administering Ad-TSH289. Subsequently, the mice underwent a four-week regimen that included oral gavage of XHXY at doses of 17 g/kg·d and 34 g/kg·d, along with intraperitoneal injections of Gentiopicroside (GPS). Utilizing the principles of pharmacological chemistry in traditional Chinese medicine, we employed high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (HPLC-QTOF/MS) to discern prescribed prototype composition of XHXY in serum samples from mouse. TMT proteomics research provided evidence of XHXY's putative targets and important pathways in vivo. The binding activity of probable action targets and prototype composition was detected by molecular docking. Finally, Immunohistochemistry (IHC) and TUNEL staining were used to verify the mechanism of XHXY and GPS in anti-GD. RESULTS XHXY and GPS alleviated GD by ameliorating the pathological changes and reducing thyroxine and TRAb levels. In mouse serum, a total of 31 prototypical XHXY ingredients were detected, and the majority of these components were from monarch and minister medicine. Proteomics study results indicated that the XHXY may mainly regulate targets including FAS-associated death domain protein (FADD), Apolipoprotein C-III, etc. and main pathways are Apoptosis, Cholesterol metabolism, TNF signalling pathway, etc. Strong binding activity of the prototypical active ingredient and GPS towards FADD, Caspase 8, and Caspase 3 was demonstrated by molecular docking. XHXY and its primary component, GPS, elevated the expression of FADD, Caspase 8, and Caspase 3, and enhance apoptosis in thyroid cells, as lastly validated by TUNEL and IHC staining. CONCLUSIONS XHXY exhibits a favorable therapeutic effect in treating GD by promoting apoptosis in thyroid cells through the upregulation of FADD, Caspase 8, and Caspase 3 expression. And GPS is the main efficacy material basis for its therapeutic effect in anti-GD.
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Affiliation(s)
- Pingping Xiang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Qinning Li
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Guoqian Cui
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Nan Xu
- Department of Traditional Chinese Medicine, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210000, China; Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qi Xiao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Xiaoyang Qu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Yunnan Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Yu Chen
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Xiao Wei
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Qifeng Wang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Ronglin Zhong
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Kemian Liu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Chao Liu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China.
| | - Fenxia Zhu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China.
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Zhou Y, Ding N, Zhang Y, Zhang H, Hong H, Luo Y, Tan Y. Plastein reaction augments the metal chelating capabilities of silver carp (Hypophthalmichthys molitrix) hydrolysates: Unlocking the chemical modification mechanism. Food Chem 2024; 438:138030. [PMID: 38000155 DOI: 10.1016/j.foodchem.2023.138030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Plastein reaction mechanisms and the alteration of its product properties have been studied for decades. This study investigated the plastein-mediated modifications in silver carp protein hydrolysate (SCPH) from both mechanistic and functional perspectives. Unlike prior research, this investigation uncovered that hydrogen bonding supplemented the dominant hydrophobic interactions in plastein's mechanism for the first time, as supported by peptide concentrations, molecular weight, amino acids, chemical forces, and peptide sequence by LC-MS/MS. This innovative reaction mechanism cascaded into the enhancement of SCPH functional attributes. Plastein induced increased COOH in SCPH's side-chain groups significantly enhanced Fe2+ (from 4.49 to 14.12 %) and Zn2+ (from 53.53 to 64.47 %) chelation. Moreover, the elevated DPPH (17.56 %-23.97 %) and hydroxyl radical (68.49 %-79.32 %) scavenging power indicated a broader improvement in SCPH with plastein. In SCPH, plastein elucidated reaction intricacies and enhanced its utility, propelling SCPH into a realm of extended potential.
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Affiliation(s)
- Yongjie Zhou
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Ning Ding
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yan Zhang
- Experimental Seafood Processing Laboratory, Coastal Research and Extension Center, Mississippi State University, Pascagoula, MS 39567, USA.
| | - Huijuan Zhang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Hui Hong
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yongkang Luo
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yuqing Tan
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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Long XB, Yao CR, Li SY, Zhang JG, Lu ZJ, Ma DD, Chen CE, Ying GG, Shi WJ. Screening androgen receptor agonists of fish species using machine learning and molecular model in NORMAN water-relevant list. J Hazard Mater 2024; 468:133844. [PMID: 38394900 DOI: 10.1016/j.jhazmat.2024.133844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Androgen receptor (AR) agonists have strong endocrine disrupting effects in fish. Most studies mainly investigate AR binding capacity using human AR in vitro. However, there is still few methods to rapidly predict AR agonists in aquatic organisms. This study aimed to screen AR agonists of fish species using machine learning and molecular models in water-relevant list from NORMAN, a network of reference laboratories for monitoring contaminants of emerging concern in the environment. In this study, machine learning approaches (e.g., Deep Forest (DF)), Random Forests and artificial neural networks) were applied to predict AR agonists. Zebrafish, fathead minnow, mosquitofish, medaka fish and grass carp are all important aquatic model organisms widely used to evaluate the toxicity of new pollutants, and the molecular models of ARs from these five fish species were constructed to further screen AR agonists using AlphaFold2. The DF method showed the best performances with 0.99 accuracy, 0.97 sensitivity and 1 precision. The Asn705, Gln711, Arg752, and Thr877 residues in human AR and the corresponding sites in ARs from the five fish species were responsible for agonist binding. Overall, 245 substances were predicted as suspect AR agonists in the five fish species, including, certain glucocorticoids, cholesterol metabolites, and cardiovascular drugs in the NORMAN list. Using machine learning and molecular modeling hybrid methods rapidly and accurately screened AR agonists in fish species, and helping evaluate their ecological risk in fish populations.
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Affiliation(s)
- Xiao-Bing Long
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Chong-Rui Yao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Si-Ying Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jin-Ge Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Zhi-Jie Lu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Dong-Dong Ma
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Chang-Er Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Wen-Jun Shi
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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Deng JW, Yuan S, Shi LP, Chen X, Liu J, Chen ZW, Tan KY, Yang Q, Cao WF. Integration of network pharmacology and serum medicinal chemistry to investigate the pharmacological mechanisms of QiZhuYangGan Decoction in the treatment of hepatic fibrosis. J Ethnopharmacol 2024; 323:117730. [PMID: 38190954 DOI: 10.1016/j.jep.2024.117730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/02/2024] [Accepted: 01/06/2024] [Indexed: 01/10/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Qizhuyanggan Decoction (QZD), a traditional Chinese medicine formula, is frequently utilized in clinical practice for managing hepatic fibrosis. However, the specific target and mechanism of action of QZD for hepatic fibrosis treatment remain unknown. AIM OF THE STUDY By combining network pharmacology, serum medicinal chemistry, and experimental validation methods, our study aimed to investigate the therapeutic effects of QZD on hepatic fibrosis, the anti-hepatic fibrosis active ingredients, and the possible mechanism of anti-hepatic fibrosis action. MATERIALS AND METHODS The study aimed to investigate the therapeutic effect of QZD on hepatic fibrosis induced by CCl4 in SD rats, as well as its mechanism of action. The rats were anesthetized intraperitoneally using 3% pentobarbital and were executed after asphyxiation with high concentrations of carbon dioxide. Several techniques were employed to evaluate the efficacy of QZD, including ELISA, Western blot, HYP reagent assay, and various pathological examinations such as HE, Masson, Sirius Red staining, and immunohistochemistry (IHC). Additionally, serum biochemical assays were conducted to assess the effect of QZD on liver injury. Network pharmacology, UPLC, molecular docking, and molecular dynamics simulation were utilized to explore the mechanism of QZD in treating hepatic fibrosis. Finally, experimental validation was performed through ELISA, IHC, RT-qPCR, and Western blot analysis. RESULT Liver histopathology showed that QZD reduced inflammation and inhibited collagen production, and QZD significantly reduced HA and LN content to treat hepatic fibrosis. Serum biochemical analysis showed that QZD improved liver injury. Network pharmacology combined with UPLC screened six active ingredients and obtained 87 targets for the intersection of active ingredients and diseases. The enrichment analysis results indicated that the PI3K/AKT pathway might be the mechanism of action of QZD in the treatment of hepatic fibrosis, and counteracting the inflammatory response might be one of the pathways of action of QZD. Molecular docking and molecular dynamics simulations showed that the active ingredient had good binding properties with PI3K, AKT, and mTOR proteins. Western blot, ELISA, PCR, and IHC results indicated that QZD may treat hepatic fibrosis by inhibiting the PI3K/AKT/mTOR pathway and suppressing M1 macrophage polarization, while also promoting M2 macrophage polarization. CONCLUSIONS QZD may be effective in the treatment of hepatic fibrosis by inhibiting the PI3K/AKT/mTOR signaling pathway and M1 macrophage polarization, while promoting M2 macrophage polarization. This provides a strong basis for the clinical application of QZD.
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Affiliation(s)
- Jing-Wei Deng
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China
| | - Su Yuan
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China; Department of Combination of Chinese and Western Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li-Peng Shi
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China
| | - Xin Chen
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China
| | - Jun Liu
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China; Department of Combination of Chinese and Western Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Wei Chen
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China
| | - Kai-Yue Tan
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China
| | - Qian Yang
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China
| | - Wen-Fu Cao
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing, China; Department of Combination of Chinese and Western Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Zhang Y, Li WW, Wang Y, Fan YW, Wang QY, Liu C, Jiang S, Shang EX, Duan JA. Investigation of the material basis and mechanism of Lizhong decoction in ameliorating ulcerative colitis based on spectrum-effect relationship and network pharmacology. J Ethnopharmacol 2024; 323:117666. [PMID: 38159822 DOI: 10.1016/j.jep.2023.117666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Lizhong decoction (LZD), a classical herbal prescription recorded by Zhang Zhongjing in Treatise on Febrile and Miscellaneous Diseases, has been extensively used to treat ulcerative colitis (UC) in clinical practice for thousands of years. However, its material basis and underlying mechanism are not yet clear. AIM OF THE STUDY This study aims to explore the material basis and potential mechanism of LZD against UC based on the spectrum-effect relationship and network pharmacology. MATERIALS AND METHODS First, LZD was extracted by a systematic solvent extraction method into four parts. Ultra-high performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) technique was used to identify the compounds from different polar parts, and dextran sulfate sodium (DSS)-induced colitis model was used to evaluate the efficacy of each fraction. Then, the spectrum-effect analyses of compounds and efficacy indicators were established via grey relational analysis (GRA), bivariate correlation analysis (BCA) and partial least squares regression (PLSR). Finally, the potential mechanism of LZD for UC therapy was explored by network pharmacology, and the results were further verified by molecular docking and reverse transcription quantitative polymerase chain reaction (RT-qPCR). RESULTS 66 chemical components of LZD were identified by UPLC-Q-TOF-MS/MS technology. The pharmacodynamic results showed that extraction parts of LZD had different therapeutic effects on UC, among which ethyl acetate and n-butanol extracts had significant anti-colitis effects, which might be the main effective fractions of LZD. Furthermore, the spectrum-effect analyses indicated that 21 active ingredients such as liquiritin apioside, neolicuroside, formononetin, ginsenoside Rg1, 6-gingesulfonic acid, licoricesaponin A3, liquiritin, glycyrrhizic acid were the main material basis for LZD improving UC. Based on the above results, network pharmacology suggested that the amelioration of LZD on UC might be closely related to the PI3K-Akt signaling pathway. Additionally, molecular docking technology and RT-qPCR further verified that LZD could markedly inhibit the PI3K-Akt signaling pathway. CONCLUSION Overall, our study first identified the chemical compositions of LZD by using UPLC-Q-TOF-MS/MS. Furthermore, the material basis and potential mechanism of LZD in improving UC were comprehensively elucidated via spectrum-effect relationships, network pharmacology, molecular docking and experimental verification. The proposed strategy provided a systematic approach for exploring how herbal medicines worked. More importantly, it laid the solid foundation for further clinical application and rational development of LZD.
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Affiliation(s)
- Yun Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Wen-Wen Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Yu Wang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Yu-Wen Fan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Qu-Yi Wang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Chen Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China.
| | - Er-Xin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China.
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Wu Y, Liu M, He X, Zhou H, Wei J, Li H, Yuan Q, Zuo Y, Zhao L, Xie Y. A breakthrough in periodontitis treatment: Revealing the pharmacodynamic substances and mechanisms of Kouqiangjie formula. J Ethnopharmacol 2024; 323:117738. [PMID: 38199336 DOI: 10.1016/j.jep.2024.117738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/29/2023] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
ETHNOPHARMACOLOGY RELEVANCE Periodontitis, a complex inflammatory disease, significantly affects people's lives. Traditional Chinese multi-herbal formulas, composed of various herbs, exhibit their therapeutic efficacy holistically. Kouqiangjie Formula (KQJF), comprising 12 herbs including Rhizoma smilacis glabrae, Polygonatum sibiricum Delar. ex Redoute, Taraxacum mongolicum Hand.-Mazz, etc., has been clinically proven to effectively treat periodontitis. However, the potential active substances conferring these effects and their mechanisms of action remain unclear. AIM OF THE STUDY The current investigation endeavours to utilize Ultra Performance Liquid Chromatography Quadrupole Time of Flight Mass Spectrometry (UPLC-Q-TOF-MS), network pharmacology, and in vivo animal experiment confirmation to explore the plausible bioactive compounds and operational mechanisms underpinning KQJF's therapeutic impact on periodontitis. MATERIALS AND METHODS Using the UPLC-Q-TOF-MS technique, we deciphered the chemical constituents of KQJF. Network pharmacology was employed to earmark key bioactive elements, forecast principal targets, and operational pathways which were later substantiated through molecular docking. Experimental validations were carried out in a periodontitis animal model using a range of techniques, including micro-CT, H&E staining, qRT-PCR, and protein blotting procedures, providing comprehensive verification of our initial assumptions. RESULTS Utilizing UPLC-Q-TOF-MS, we characterized 87 individual chemical constituents in KQJF. Network pharmacology revealed that 14 components, including senkyunolide A, glycycoumarin, licoflavonol, glycyrin, senkyunolide I, and senkyunolide H, form the key therapeutic basis of KQJF in targeting periodontitis. Significant targets and pathways were discerned as AKT1, MMP9, JUN, PTGS2, CASP3, TLR4, IL1β, BCL2, PPARG, and pathways such as the TNF signaling pathway, NF-κB signaling pathway, osteoclast differentiation, and Wnt signaling pathway. Molecular docking demonstrated robust binding activity between these crucial targets and the key active ingredients. In vivo experimentation corroborated that, compared with the model group, KQJF significantly ameliorated symptoms and micro-CT imaging parameters of periodontitis in the rat model, down-regulating the expression of AKT1, MMP9, JUN, PTGS2, CASP3, TLR4, and IL1β, while up-regulating the expression of BCL2 and PPARG. CONCLUSION In summary, this study has pioneered a comprehensive exploration of the potential therapeutic constituents, targets, and mechanisms of KQJF for periodontitis treatment, adopting a synergistic strategy of "chemical component analysis-network pharmacology screening-in vivo animal experiment validation". This provides experimental evidence for the clinical application of KQJF and further in-depth research. Additionally, it presents an effective strategy for the research of other Chinese herbal formulations.
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Affiliation(s)
- Yeke Wu
- Department of Stomatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Min Liu
- Department of Gynaecology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Xiang He
- Department of Stomatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Hongling Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jing Wei
- Department of Stomatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Huijing Li
- Department of Stomatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Qianghua Yuan
- Department of Pharmacy, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Yuling Zuo
- Department of Stomatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Lixing Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Yunfei Xie
- Department of Nuclear Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
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Yang J, Qin L, Zhou S, Li J, Tu Y, Mo M, Liu X, Huang J, Qin X, Jiao A, Wei W, Yang P. Network pharmacology, molecular docking and experimental study of CEP in nasopharyngeal carcinoma. J Ethnopharmacol 2024; 323:117667. [PMID: 38159821 DOI: 10.1016/j.jep.2023.117667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/17/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The Stephania cephalantha Hayata is an important traditional medicinal plant widely used in traditional medicine to treat cancer. Cepharanthine (CEP) was extracted from the roots of Stephania cephalantha Hayata. It has been found to exhibit anticancer activity in different types of cancer cells. Nevertheless, the activity of CEP against nasopharyngeal carcinoma (NPC) and its underlying mechanism warrant further investigation. AIMS OF THE STUDY NPC is an invasive and highly metastatic malignancy that affects the head and neck region. This research aimed to investigate the pharmacological properties and underlying mechanism of CEP against NPC, aiming to offer novel perspectives on treating NPC using CEP. MATERIALS AND METHODS In vitro, the pharmacological activity of CEP against NPC was evaluated using the CCK-8 assay. To predict and elucidate the anticancer mechanism of CEP against NPC, we employed network pharmacology, conducted molecular docking analysis, and performed Western blot experiments. In vivo validation was performed through a nude mice xenograft model of human NPC, Western blot and immunohistochemical (IHC) assays to confirm pharmacological activity and the mechanism. RESULTS In a dose-dependent manner, the proliferation and clonogenic capacity of NPC cells were significantly inhibited by CEP. Additionally, NPC cell migration was suppressed by CEP. The results obtained from network pharmacology experiments revealed that anti-NPC effect of CEP was associated with 8 core targets, including EGFR, AKT1, PIK3CA, and mTOR. By performing molecular docking, the binding capacity of CEP to the candidate core proteins (EGFR, AKT1, PIK3CA, and mTOR) was predicted, resulting in docking energies of -10.0 kcal/mol for EGFR, -12.4 kcal/mol for PIK3CA, -10.8 kcal/mol for AKT1, and -8.6 kcal/mol for mTOR. The Western blot analysis showed that CEP effectively suppressed the expression of EGFR and the phosphorylation levels of downstream signaling proteins, including PI3K, AKT, mTOR, and ERK. After CEP intervention, a noteworthy decrease in tumor size, without inducing any toxicity, was observed in NPC xenograft nude mice undergoing in vivo treatment. Additionally, IHC analysis demonstrated a significant reduction in the expression levels of EGFR and Ki-67 following CEP treatment. CONCLUSION CEP exhibits significant pharmacological effects on NPC, and its mechanistic action involves restraining the activation of the EGFR/PI3K/AKT pathway. CEP represents a promising pharmaceutical agent for addressing and mitigating NPC.
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Affiliation(s)
- Jiangping Yang
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Liujie Qin
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, China
| | - Shouchang Zhou
- Life Sciences Institute, Guangxi Medical University, Nanning, 530021, China
| | - Jixing Li
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Yu Tu
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Minfeng Mo
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Xuenian Liu
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Jinglun Huang
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Xiumei Qin
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Aijun Jiao
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China; Life Sciences Institute, Guangxi Medical University, Nanning, 530021, China.
| | - Wei Wei
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China.
| | - Peilin Yang
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China.
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Liu Y, Wu Y, Wang L, Zhu L, Dong Y, Xu W. A ratiometric dual-fluorescent paper-based synthetic biosensor for visual detection of tetracycline on-site. J Hazard Mater 2024; 467:133647. [PMID: 38335608 DOI: 10.1016/j.jhazmat.2024.133647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
The excessive use of tetracycline poses a threat to human health, making it essential to monitor and regulate its usage. While whole-cell biosensors offer a simple and cost-effective method, their utility is constrained by limitations in sensitivity, portability, and robustness, hindering real-time measurements within complex environmental contexts. In this study, a ratiometric i/cTetR synthetic biosensing test strip with an engineered modified dual-fluorescence reporting was developed for detecting Tet antibiotics in water and food. First, the standardized unidirectional promoter PtetR by tailoring and screening TetR transcription factor binding sites and verified by molecular docking, shortening the detection time. Secondly, decoupling the sensing and reporting modules enhances the biosensor's performance, eliminating genetic background leakage and tripling the output signal. Thirdly, a ratiometric dual fluorescence signal i/cTetR biosensing test strip was designed. Under the light box LED/UV light source, the dual signal output method significantly reduced false negative results and enhanced the anti-interference capability of the biosensor. The i/cTetR strips can detect Tet in tap water (5-1280 μg/mL) and milk (50-3200 μg/kg) within 45 min in high volume on-site without separation and purification. This study provides a standardized and universal sensing method for the field detection of antibiotic contaminants.
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Affiliation(s)
- Yanger Liu
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China; Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yifan Wu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lei Wang
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yulan Dong
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Wentao Xu
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China; Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, People's Republic of China.
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Zhang X, Liu L, Wang Y, Yu Y, Cheng W, Xu B, Xiao F. Insight into the binding characteristics of epigallocatechin-3-O-gallate and alcohol dehydrogenase: Based on the spectroscopic and molecular docking analysis. Spectrochim Acta A Mol Biomol Spectrosc 2024; 310:123943. [PMID: 38277788 DOI: 10.1016/j.saa.2024.123943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/25/2023] [Accepted: 01/21/2024] [Indexed: 01/28/2024]
Abstract
Alcohol dehydrogenase (ADH) is one of the pivotal enzymes for alcohol metabolism, which plays an important role in many physiological processes. In this study, the activation effects of epigallocatechin-3-O-gallate (EGCG) on ADH and the characteristics of the interaction were investigated via biochemical method, spectroscopy methods, and molecular docking. The results demonstrated that EGCG significantly increased the catalytic activity of ADH with a 33.33% activation rate and that EGCG blending slightly altered the microenvironment surrounding ADH aromatic amino acids, with an increase in the quantity of β-sheet and a decrease in the α-helix. Through the thermal stability analysis, it is further shown that the interaction of the two affects the intra-molecular hydrogen bond formation of the protein, and the conformation is partially extended. Besides, a total of 8 residues in ADH participated in the docking with EGCG, among which Asp-227, Lys-231, Glu-234, Gly-365 and Glu-366 participated in the formation of hydrogen bonds. At the same time, EGCG and amino group of Lys-231 form a noncovalent bond through cation-π interaction. In particular, hydrogen bonding was beneficial to keep the stability of EGCG-ADH, which was the primary driver of ADH activity activation. The results supply a new way for EGCG to activate ADH and a theoretical basis for the development of anti-alcoholism products.
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Affiliation(s)
- Xiaodan Zhang
- College of Food and Bioengineering, National Experimental Teaching Demonstration Center for Food Processing and Security, Henan Engineering Technology Research Center of Food Raw Materials, International Joint Laboratory of Food Processing and Quality Safety Control of Henan Province, Henan Engineering Technology Research Center of Food Microbiology, Henan University of Science and Technology, Luoyang 471023, PR China
| | - Lili Liu
- College of Food and Bioengineering, National Experimental Teaching Demonstration Center for Food Processing and Security, Henan Engineering Technology Research Center of Food Raw Materials, International Joint Laboratory of Food Processing and Quality Safety Control of Henan Province, Henan Engineering Technology Research Center of Food Microbiology, Henan University of Science and Technology, Luoyang 471023, PR China.
| | - Yuantu Wang
- College of Food and Bioengineering, National Experimental Teaching Demonstration Center for Food Processing and Security, Henan Engineering Technology Research Center of Food Raw Materials, International Joint Laboratory of Food Processing and Quality Safety Control of Henan Province, Henan Engineering Technology Research Center of Food Microbiology, Henan University of Science and Technology, Luoyang 471023, PR China
| | - Ying Yu
- College of Food and Bioengineering, National Experimental Teaching Demonstration Center for Food Processing and Security, Henan Engineering Technology Research Center of Food Raw Materials, International Joint Laboratory of Food Processing and Quality Safety Control of Henan Province, Henan Engineering Technology Research Center of Food Microbiology, Henan University of Science and Technology, Luoyang 471023, PR China
| | - Weiwei Cheng
- College of Food and Bioengineering, National Experimental Teaching Demonstration Center for Food Processing and Security, Henan Engineering Technology Research Center of Food Raw Materials, International Joint Laboratory of Food Processing and Quality Safety Control of Henan Province, Henan Engineering Technology Research Center of Food Microbiology, Henan University of Science and Technology, Luoyang 471023, PR China.
| | - Baocheng Xu
- College of Food and Bioengineering, National Experimental Teaching Demonstration Center for Food Processing and Security, Henan Engineering Technology Research Center of Food Raw Materials, International Joint Laboratory of Food Processing and Quality Safety Control of Henan Province, Henan Engineering Technology Research Center of Food Microbiology, Henan University of Science and Technology, Luoyang 471023, PR China
| | - Feng Xiao
- College of Food and Bioengineering, National Experimental Teaching Demonstration Center for Food Processing and Security, Henan Engineering Technology Research Center of Food Raw Materials, International Joint Laboratory of Food Processing and Quality Safety Control of Henan Province, Henan Engineering Technology Research Center of Food Microbiology, Henan University of Science and Technology, Luoyang 471023, PR China
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Lu Z, Yang J, Xu X, Liu R, Lin S. Regulation mechanisms of sea cucumber peptides against scopolamine-induced memory disorder and novel memory-improving peptides identification. Eur J Pharmacol 2024; 968:176430. [PMID: 38369274 DOI: 10.1016/j.ejphar.2024.176430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 01/04/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Memory impairment affects cognition and information processing, and attention, leading to a decline in life quality of patients. Previous studies have shown the memory-improving effects of sea cucumber peptides. This study further explored the memory-improving mechanisms of sea cucumber peptides using scopolamine-induced memory-impaired mice and identified novel memory-improving peptides within low molecular weight peptide fractions. The sea cucumber peptides were categorized into three groups based on their molecular weights: SCP-L (molecular weight greater than 10 kDa), SCP-M (weight between 3 kDa and 10 kDa), and SCP-S (molecular weight less than 3 kDa). The results showed that SCP-S improved behavioral performance by regulating cholinergic system disorder and reducing oxidative stress levels, distinguishing itself from SCP-M and SCP-L. Further, SCP-S was found to exhibit a well ability in alleviating the degree of neuroinflammation dependent on microglia and promoting synaptic plasticity. Additionally, a novel memory-improving peptide Ser-Phe-Gly-Asp-Ile (SFGDI) was identified by EASY-nano-LC/MS/MS after simulated digestion-absorption coupling of in silico technologies from SCP-S. SFGDI protected against oxidative stress and regulated cholinergic system in scopolamine-induced PC12 cells. These findings suggest that SCP-S and SFGDI might be considered as potential memory-improving food for people suffering from memory disorders.
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Affiliation(s)
- Zhiqiang Lu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China; Engineering Research Center of Special Dietary Food of Liaoning Province, Food Engineering Technology Research Center of Liaoning Province, Dalian, 116034, PR China
| | - Jingqi Yang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China; Engineering Research Center of Special Dietary Food of Liaoning Province, Food Engineering Technology Research Center of Liaoning Province, Dalian, 116034, PR China
| | - Xiaomeng Xu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China; Engineering Research Center of Special Dietary Food of Liaoning Province, Food Engineering Technology Research Center of Liaoning Province, Dalian, 116034, PR China
| | - Ruowen Liu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China; Engineering Research Center of Special Dietary Food of Liaoning Province, Food Engineering Technology Research Center of Liaoning Province, Dalian, 116034, PR China
| | - Songyi Lin
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China; Engineering Research Center of Special Dietary Food of Liaoning Province, Food Engineering Technology Research Center of Liaoning Province, Dalian, 116034, PR China.
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Ngueanngam N, Jityuti B, Patnin S, Boonsri P, Makarasen A, Buranaprapuk A. Multiple spectroscopic and computational studies on binding interaction of 2-phenylamino-4-phenoxyquinoline derivatives with bovine serum albumin. Spectrochim Acta A Mol Biomol Spectrosc 2024; 310:123948. [PMID: 38309006 DOI: 10.1016/j.saa.2024.123948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/05/2024]
Abstract
Binding characteristics of potent non-nucleoside HIV-1 reverse transcriptase inhibitors, 4-(2',6'-dimethyl-4'-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (1) and 4-(2',6'-dimethyl-4'-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (2), to bovine serum albumin (BSA) under simulative physiological conditions were investigated by multiple spectroscopic and computational methods. The experimental results demonstrated that (1) and (2) bound to BSA at site III (subdomain IB), and quenched BSA fluorescence through a static quenching process. The binding interaction of (1) or (2) to BSA forms stable complexes with the binding constants (Kb) at the level of 104 L/mol and the number of binding site was determined to be 1 for both systems, indicating that new synthesized compounds occupied one site in BSA with moderate binding affinities. Based on the analysis of the thermodynamic parameters, it can be indicated that the main binding forces for interaction between BSA and both compounds were hydrogen bonding and van der Waals force. Synchronous fluorescence results revealed that the interaction of two compounds with BSA led to modifications in the microenvironment surrounding tryptophan residue of BSA. Circular dichroism spectra demonstrated alterations in the secondary structure of BSA induced by (1) and (2). Moreover, the experimental data of molecular docking and molecular dynamics (MD) simulations supported the results obtained from multiple spectroscopic techniques, confirming the binding interactions between both compounds and BSA.
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Affiliation(s)
- Natchaphon Ngueanngam
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Benchawan Jityuti
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Suwicha Patnin
- Department of Chemistry, Laboratory of Organic Synthesis, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Pornthip Boonsri
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Arthit Makarasen
- Department of Chemistry, Laboratory of Organic Synthesis, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Apinya Buranaprapuk
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand.
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Sankar S, Kodiveri Muthukaliannan G. Deciphering the crosstalk between inflammation and biofilm in chronic wound healing: Phytocompounds loaded bionanomaterials as therapeutics. Saudi J Biol Sci 2024; 31:103963. [PMID: 38425782 PMCID: PMC10904202 DOI: 10.1016/j.sjbs.2024.103963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024] Open
Abstract
In terms of the economics and public health, chronic wounds exert a significant detrimental impact on the health care system. Bacterial infections, which cause the formation of highly resistant biofilms that elude standard antibiotics, are the main cause of chronic, non-healing wounds. Numerous studies have shown that phytochemicals are effective in treating a variety of diseases, and traditional medicinal plants often include important chemical groups such alkaloids, phenolics, tannins, terpenes, steroids, flavonoids, glycosides, and fatty acids. These substances are essential for scavenging free radicals which helps in reducing inflammation, fending off infections, and hastening the healing of wounds. Bacterial species can survive in chronic wound conditions because biofilms employ quorum sensing as a communication technique which regulates the expression of virulence components. Fortunately, several phytochemicals have anti-QS characteristics that efficiently block QS pathways, prevent drug-resistant strains, and reduce biofilm development in chronic wounds. This review emphasizes the potential of phytocompounds as crucial agents for alleviating bacterial infections and promoting wound healing by reducing the inflammation in chronic wounds, exhibiting potential avenues for future therapeutic approaches to mitigate the healthcare burden provided by these challenging conditions.
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Affiliation(s)
- Srivarshini Sankar
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
| | - Gothandam Kodiveri Muthukaliannan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
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Zhu J, Meng H, Li X, Jia L, Xu L, Cai Y, Chen Y, Jin J, Yu L. Optimization of virtual screening against phosphoinositide 3-kinase delta: Integration of common feature pharmacophore and multicomplex-based molecular docking. Comput Biol Chem 2024; 109:108011. [PMID: 38198965 DOI: 10.1016/j.compbiolchem.2023.108011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
Extensive research has accumulated which suggests that phosphatidylinositol 3-kinase delta (PI3Kδ) is closely related to the occurrence and development of various human diseases, making PI3Kδ a highly promising drug target. However, PI3Kδ exhibits high homology with other members of the PI3K family, which poses significant challenges to the development of PI3Kδ inhibitors. Therefore, in the present study, a hybrid virtual screening (VS) approach based on a ligand-based pharmacophore model and multicomplex-based molecular docking was developed to find novel PI3Kδ inhibitors. 13 crystal structures of the human PI3Kδ-inhibitor complex were collected to establish models. The inhibitors were extracted from the crystal structures to generate the common feature pharmacophore. The crystallographic protein structures were used to construct a naïve Bayesian classification model that integrates molecular docking based on multiple PI3Kδ conformations. Subsequently, three VS protocols involving sequential or parallel molecular docking and pharmacophore approaches were employed. External predictions demonstrated that the protocol combining molecular docking and pharmacophore resulted in a significant improvement in the enrichment of active PI3Kδ inhibitors. Finally, the optimal VS method was utilized for virtual screening against a large chemical database, and some potential hit compounds were identified. We hope that the developed VS strategy will provide valuable guidance for the discovery of novel PI3Kδ inhibitors.
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Affiliation(s)
- Jingyu Zhu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Huiqin Meng
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xintong Li
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lei Jia
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Yanfei Cai
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yun Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Jin
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Li Yu
- School of Inspection and Testing Certification, Changzhou Vocational Institute of Engineering, Changzhou, Jiangsu 213164, China.
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Shellenberger BM, Basile ON, Cassel J, Olsen MR, Salvino JM, Montaner LJ, Tietjen I, Henry GE. Synthesis, SARS-CoV-2 main protease inhibition, molecular docking and in silico ADME studies of furanochromene-quinoline hydrazone derivatives. Bioorg Med Chem Lett 2024; 102:129679. [PMID: 38423371 DOI: 10.1016/j.bmcl.2024.129679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Seven furanochromene-quinoline derivatives containing a hydrazone linker were synthesized by condensing a furanochromene hydrazide with quinoline 2-, 3-, 4-, 5-, 6-, and 8-carbaldehydes, including 8-hydroxyquinoline-2-carbaldehye. Structure-activity correlations were investigated to determine the influence of the location of the hydrazone linker on the quinoline unit on SARS-CoV-2 Mpro enzyme inhibition. The 3-, 5-, 6- and 8-substituted derivatives showed moderate inhibition of SARS-CoV-2 Mpro with IC50 values ranging from 16 to 44 μM. Additionally, all of the derivatives showed strong interaction with the SARS-CoV-2 Mpro substrate binding pocket, with docking energy scores ranging from -8.0 to -8.5 kcal/mol. These values are comparable to that of N3 peptide (-8.1 kcal/mol) and more favorable than GC-373 (-7.6 kcal/mol) and ML-188 (-7.5 kcal/mol), all of which are known SARS-CoV-2 Mpro inhibitors. Furthermore, in silico absorption, distribution, metabolism, and excretion (ADME) profiles indicate that the derivatives have good drug-likeness properties. Overall, this study highlights the potential of the furanochromene-quinoline hydrazone scaffold as a SARS-CoV-2 Mpro inhibitor.
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Affiliation(s)
- Blake M Shellenberger
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Olivia N Basile
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Joel Cassel
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Morgan R Olsen
- Department of Chemistry, Bucknell University, One Dent Drive, Lewisburg, PA 17837, USA
| | | | | | - Ian Tietjen
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Geneive E Henry
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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Darvishi F, Beiranvand E, Kalhor H, Shahbazi B, Mafakher L. Homology modeling and molecular docking studies to decrease glutamine affinity of Yarrowia lipolytica L-asparaginase. Int J Biol Macromol 2024; 263:130312. [PMID: 38403216 DOI: 10.1016/j.ijbiomac.2024.130312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/10/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
L-Asparaginase is a key component in the treatment of leukemias and lymphomas. However, the glutamine affinity of this therapeutic enzyme is an off-target activity that causes several side effects. The modeling and molecular docking study of Yarrowia lipolytica L-asparaginase (YL-ASNase) to reduce its l-glutamine affinity and increase its stability was the aim of this study. Protein-ligand interactions of wild-type and different mutants of YL-ASNase against L-asparagine compared to l-glutamine were assessed using AutoDock Vina tools because the crystal structure of YL-ASNase does not exist in the protein data banks. The results showed that three mutants, T171S, T171S-N60A, and T171A-T223A, caused a considerable increase in L-asparagine affinity and a decrease in l-glutamine affinity as compared to the wild-type and other mutants. Then, molecular dynamics simulation and MM/GBSA free energy were applied to assess the stability of protein structure and its interaction with ligands. The three mutated proteins, especially T171S-N60A, had higher stability and interactions with L-asparagine than l-glutamine in comparison with the wild-type. The YL-ASNase mutants could be introduced as appropriate therapeutic candidates that might cause lower side effects. However, the functional properties of these mutated enzymes need to be confirmed by genetic manipulation and in vitro and in vivo studies.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran.
| | - Elham Beiranvand
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Hourieh Kalhor
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Behzad Shahbazi
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
| | - Ladan Mafakher
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Aminu KS, Uzairu A, Abechi SE, Shallangwa GA, Umar AB. Activity prediction, structure-based drug design, molecular docking, and pharmacokinetic studies of 1,4-dihydropyridines derivatives as α-amylase inhibitors. J Taibah Univ Med Sci 2024; 19:270-286. [PMID: 38234713 PMCID: PMC10793175 DOI: 10.1016/j.jtumed.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/16/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024] Open
Abstract
Objectives Diabetes places a substantial economic burden on countries worldwide. The costs associated with diabetes management, including healthcare services, medications, monitoring equipment, and productivity losses, are substantial. The International Diabetes Federation has estimated that global healthcare expenditures associated with diabetes and its complications exceed hundreds of billions of dollars annually. Therefore, a critical need exists to develop drugs that are highly effective, affordable, and easily accessible to society. Methods This study explored the structural modification of 1,4-DHP derivatives to identify specific α-amylase inhibitors, with the aim of developing more effective and accessible drugs for diabetes. We evaluated the activity and binding ability of the designed compounds. In addition, we performed drug-likeness and pharmacokinetic studies on the modified compounds. Results Equation (1) had the highest accuracy, on the basis of internal and external assessment parameters, including R2int = 0.852, R2adj = 0.803, Q2cv = 0.731, and R2ext = 0.884. Moreover, the five potent analogs identified through structure-based drug design demonstrated a more favorable interaction than observed for the template or acarbose. Additionally, comprehensive studies on the drug-like properties and pharmacokinetics of the designed compounds supported their oral safety and favorable pharmacokinetic profiles. Conclusions The designed analogs show promise for developing new hypoglycemic agents. Their positive attributes and performance suggest that they may potentially serve as candidates for further research in improving treatments for high blood sugar-associated conditions.
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Affiliation(s)
- Khalifa S. Aminu
- Department of Chemistry, Ahmadu Bello University, Zaria, Nigeria
- Department of Pure and Industrial Chemistry, Bayero University, Kano, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Ahmadu Bello University, Zaria, Nigeria
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Yang J, Zhang M, Luo Y, Xu F, Gao F, Sun Y, Yang B, Kuang H. Protopine ameliorates OVA-induced asthma through modulatingTLR4/MyD88/NF-κB pathway and NLRP3 inflammasome-mediated pyroptosis. Phytomedicine 2024; 126:155410. [PMID: 38367422 DOI: 10.1016/j.phymed.2024.155410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/05/2024] [Accepted: 02/01/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Chronic airway inflammation and hyperresponsiveness are characteristics of asthma. The isoquinoline alkaloid protopine (PRO) has been shown to exert anti-inflammatory effects, but its mechanism of action in asthma is not known. PURPOSE Investigate the protective properties of PRO upon asthma and elucidate its mechanism. STUDY DESIGN AND METHODS The effects of PRO in asthma treatment were assessed by histology, biochemical analysis, and real-time reverse transcription-quantitative polymerase chain reaction. Then, we integrated molecular docking, western blotting, cellular experiments, immunohistochemistry, immunofluorescence analysis, flow cytometry, and metabolomics analysis to reveal its mechanism. RESULTS In vivo, PRO therapy reduced the number of inflammatory cells (eosinophils, leukocytes, monocytes) in bronchoalveolar lavage fluid (BALF), ameliorated pathologic alterations in lung tissues, and inhibited secretion of IgG and histamine. Molecular docking showed that PRO could dock with the proteins of TLR4, MyD88, TRAF6, TAK1, IKKα, and TNF-α. Western blotting displayed that PRO inhibited the TLR4/NF-κB signaling pathway. PRO regulated expression of the pyroptosis-related proteins NLR family pyrin domain containing 3 (NLRP3) inflammasome, gasdermin D, caspase-1, and drove caspase-1 inactivation to affect inflammatory responses by inhibiting the NLRP3 inflammasome. In vitro, 24 h after treatment with PRO, cell activity, as well as levels of reactive oxygen species (ROS) and interleukin (IL)-1β and IL-18, decreased significantly. Immunofluorescence staining showed that PRO decreased expression of TLR4 and MyD88 in vitro. PRO decreased nuclear translocation of NF-κB p65. Twenty-one potential biomarkers in serum were identified using metabolomics analysis, and they predominantly controlled the metabolism of phenylalanine, tryptophan, glucose, and sphingolipids. CONCLUSION PRO reduced OVA-induced asthma. The underlying mechanism was associated with the TLR4/MyD88/NF-κB pathway and NLRP3 inflammasome-mediated pyroptosis.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Meixian Zhang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Yumeng Luo
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Feng Xu
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Fan Gao
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Yanping Sun
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Bingyou Yang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Haixue Kuang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin 150040, China.
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Abd-Rabo ZS, George RF, Zaafar DK, Gawish AY, Serry AM. Design, synthesis, and biological evaluation of some new 2-phenyl-3,6-pyridazinedione derivatives as PDE-5 inhibitors. Bioorg Chem 2024; 145:107213. [PMID: 38368658 DOI: 10.1016/j.bioorg.2024.107213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
Various 2-phenyl-3,6-pyridazinedione derivatives 4a-j, 5a-c, 6a,b, 7a-c, 8, 9, 10a-d, and 11a-d, were effectivelysynthesized, and tested for their potential inhibition of phosphodiesterase enzyme at 10 µM. Then fourteen compounds exhibiting the highest inhibition 4b, 4d, 4e, 4g, 4h, 4i, 5a, 6a,b, 7c, 10a,b, 11a, and 11d were selected for screening their PDE-5 inhibition, where compounds 4b,g,h, and 11a revealed promising PDE-5 inhibition having IC50 values = 25, 53, 22, and 42 nM, respectively in comparison with Sildenafil (IC50 = 16 nM). Additionally, these four most active compounds were safe to normal fibroblast cell line WI-38. Moreover, 4f, 4h, 4j, 10d, and 11d had almost the same anti-proliferative effect against the aortic cell line as Sildenafil. Furthermore, molecular docking illustrated that the binding of the target compounds with the key amino acids in the binding site of PDE-5 (PDB 2H42) was like to that of the cocrystallized ligand Sildenafil. Additionally, molecular dynamics simulation for the most active compound 4h revealed high stability of the 4h -PDE5 complex explaining its promising activity as a PDE-5 inhibitor. Therefore, the 2-phenyl-3,6-pyridazinedione scaffold can be considered an important core for designing more promising PDE-5 inhibitors.
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Affiliation(s)
- Zeinab S Abd-Rabo
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI, Cairo 11571, Egypt
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
| | - Dalia K Zaafar
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Modern University for Technology and Information MTI, Cairo 11571, Egypt
| | - Aya Y Gawish
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Modern University for Technology and Information MTI, Cairo 11571, Egypt
| | - Aya M Serry
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI, Cairo 11571, Egypt
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Li Y, Kowah JAH, Jiang M, Wu Y, Wang L, Yang F. Synthesis, antibacterial activity, and 3D-QASR studies of matrine-indole derivatives as potential antibiotics. Bioorg Med Chem Lett 2024; 102:129671. [PMID: 38387690 DOI: 10.1016/j.bmcl.2024.129671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Matrine and indole have antibacterial, anticancer, and other biological activities, in order to develop new antibiotics to solve the problem of multi-drug resistant bacteria. In this paper, we synthesized a series of 29 novel matrine derivatives as potential drug candidates by combining indole analogs and matrine. The antibacterial activity of these compounds was evaluated through minimum inhibitory concentration (MIC) assays against five bacterial strains (S. aureus, C. albicans, P. acnes, P. aeruginosa, and E. coli). The obtained results demonstrated promising antibacterial efficacy, particularly for compounds A20 and A18, which exhibited MICs.au values of 0.021 and 0.031 mg/ml, respectively, against S. aureus. Moreover, compounds A20 and A27 displayed remarkable MICc.al values of 2.806 and 4.519 mg/ml, respectively, against C. albicans, surpassing the performance of the clinical antibiotic penicillin G sodium (0.0368 mg/ml) and fluconazole (4.849 mg/ml). These findings underscore the significant bacteriostatic activity of the matrine derivatives. Furthermore, to gain a deeper understanding 3D-QSAR modeling was employed, revealing the critical influence of steric structure, charge distribution, hydrophobic interactions, and hydrogen bonding within the molecular structure on the bacteriostatic activity of the compounds. Additionally, molecular docking simulations shed light on the interaction between compound A20 and bacterial proteins, highlighting the involvement of hydrogen bonding, hydrophobic interactions, and π-π conjugation in the formation of stable complexes that inhibit the normal functioning of the proteins. This comprehensive analysis provided valuable insights into the antibacterial mechanism of the novel matrine derivatives, offering theoretical support for their potential application as antibiotics.
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Affiliation(s)
- Yufang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
| | - Jamal A H Kowah
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Meiyan Jiang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yaqing Wu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Lisheng Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China; Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning 530004, China.
| | - Fangfang Yang
- Guangxi - ASEAN Food Inspection and Testing Center, Nanning 530021, China
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Elgammal WE, Halawa AH, Eissa IH, Elkady H, Metwaly AM, Hassan SM, El-Agrody AM. Design, synthesis, and anticancer evaluation of N-sulfonylpiperidines as potential VEGFR-2 inhibitors, apoptotic inducers. Bioorg Chem 2024; 145:107157. [PMID: 38340473 DOI: 10.1016/j.bioorg.2024.107157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
A new panel of N-sulfonylpiperidine derivatives has been designed and synthesized as vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors. Anti-proliferative activities of the synthesized members were tested against colorectal carcinoma (HCT-116), hepatocellular carcinoma (HepG-2), and breast cancer (MCF-7) cell lines. Compounds 3a, 4, 8, and 9 showed the highest activities against the tested cell lines. In particular, compound 8 showed excellent activities against HCT-116, HepG-2, and MCF-7 with IC50 values of 3.94, 3.76, and 4.43 μM, respectively. Such IC50 values are comparable to vinblastine (IC50 = 3.21, 7.35, 5.83 μM, respectively) and doxorubicin (IC50 = 6.74, 7.52, 8.19 μM, respectively). In vitro VEGFR-2 inhibitory activity of the most promising molecules (3a, 4, 8, and 9) indicated that compound 8 is the highest VEGFR-2 inhibitor with an IC50 of 0.0554 μM, compared to sorafenib (IC50 = 0.0416 μM). The most promising candidates (3a, 4, 8, and 9) were subjected to flow cytometry analyses to assess their effects on the cell cycle behavior and the apoptotic power against the three tested cell lines (HCT-116, HepG-2, and MCF-7). The tested compound arrested the tumor cells at both the G2/M and Pre-G1 phases. In addition, compound 9 was proved as the most effective apoptotic inducer among the tested compounds against the tested cells. Molecular docking studies against VEGFR-2 (PDB ID: 2OH4) revealed good binding modes of the synthesized compound similar to that of sorafenib. Computational investigation of ADMET parameters revealed the drug-likeness of the synthesized compounds.
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Affiliation(s)
- Walid E Elgammal
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt.
| | - Ahmed H Halawa
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed M Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt; Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Saber M Hassan
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Ahmed M El-Agrody
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
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